Catalogue of Molecular Biology Programs Release 6.1 23 Jul 1999 All thanks are in the file biocatal.thanks. ===================================================================== AC BC00164 NAME WORDUP DOMAIN Pattern Identification DESCRIPTION The huge production of nucleic acid sequences has generated an DESCRIPTION impelling need for specific algorithms aimed at decoding the DESCRIPTION genetic information written in the DNA. In a previous paper, DESCRIPTION Pesole et al. (1992) presented WORDUP method which is based on a DESCRIPTION first order Markov analysis and allows us to detect statistically DESCRIPTION significant sequence motifs from six to ten nucleotides long in DESCRIPTION the sequences under investigation. DESCRIPTION We present here an improvement of the previous algorithm. The DESCRIPTION lastest version allows us to dynamically detect significant DESCRIPTION signals of any length in the same analysis. The problem addressed DESCRIPTION is the singling out of short nucleic sequences with non-random DESCRIPTION statistical properties, which may be thus biologically active. DESCRIPTION The key element in the processing is the use of a statistical DESCRIPTION analysis based on a special chi square test between the pattern DESCRIPTION of observed frequencies and of that of frequencies assessed with DESCRIPTION probability calculation. The statistical significance of each DESCRIPTION pattern is determined by comparing the expected number of DESCRIPTION sequences containing a given pattern with the observed one. DESCRIPTION The results are then futher tested to reject the falsely DESCRIPTION significant patterns, caused by partial overlapping with the DESCRIPTION true biological signal searched. The problem was solved by DESCRIPTION starting from the analysis of shorter oligomers and, through DESCRIPTION subsequent interactions, by checking that the oligomers resulting DESCRIPTION as statistically significant are not actually components of DESCRIPTION longer biological signals. DESCRIPTION The theoretical and practical importance of this method resides DESCRIPTION in the application of a very fast string matching algorithm DESCRIPTION (FastPat). The algorithm was adjusted to suit the specific DESCRIPTION requirements of biolgical research, whereby both the pattern and DESCRIPTION the sequences are compressed so that the natural four letter DESCRIPTION alphabet of DNA sequences is considerably enlarged. The novelty DESCRIPTION of this method is that it does not require of a priori alignment DESCRIPTION of the sequences to be analysed, and it performs an accurate DESCRIPTION statistical analysis accounting for the non-random sequence of DESCRIPTION the four nucleotides in the DNA. AUTHOR Pesole,Prunella,Liuni,Attimonelli,Saccone RA Pesole, G., Prunella, N., Liuni, S., Attimonelli, M. and Saccone C.; RT "WORDUP: an efficient algorithm for discovering statistically RT significant patterns in DNA sequences."; RL Nucleic Acids Res. 20:2871-2875 (1992). ADDRESS Sabino Liuni ADDRESS Area di Ricerca CNR ADDRESS Via Amendola 166/5 ADDRESS 70126 Bari(Italy) CONTACT sabino@area.ba.cnr.it SITE ftp anonymous area.ba.cnr.it SITE Directory /pub/embnet/software/wordup SITE-CONTACT sabino@area.ba.cnr.it OS Unix LANGUAGE C VOLUME - AC BC00217 NAME ANREP DOMAIN Sequence analysis DESCRIPTION ANREP is a system for approximate network regular DESCRIPTION expression pattern matching, AUTHOR Gerhard Mehldau, Eugene Myers RA Mehldau G., Myers G.; RT "A system for pattern matching applications on biosequences."; RL Comput. Appl. Biosci. 9:299-314(1993). RX Medline; 93313698. RX SeqAnalRef; MEHG9301. ADDRESS Department of Computer Science ADDRESS The University of Arizona,Tucson, Arizona 85721, USA CONTACT gene@cs.arizona.edu SITE ftp anonymous cs.arizona.edu SITE Directory /anrep SITE-CONTACT lab@cs.arizona.edu OS Unix LANGUAGE C VOLUME - REQUIRES - COMMENTS From the authors : COMMENTS ANREP is a prototype system. We are interested in seeing our COMMENTS system used and consequently are willing to fix problems as our COMMENTS time permits. We make no warrants or guarantees however. AC BC00218 NAME BIGPROBE DOMAIN Sequence analysis AUTHOR - RT - ADDRESS University of Arizona Genetics Software Center ADDRESS Molecular & Cellular Biology, USA CONTACT kmwillia@joplin.biosci.arizona.edu SITE ftp anonymous joplin.biosci.arizona.edu SITE-CONTACT Directory /pub/seq_analysis/bprobe OS IBM PC or clone, MS-DOS/PC-DOS IBM PS/2, OS Sun-3, Unix LANGUAGE C C VOLUME - AC BC00219 NAME CODECOUNT DOMAIN Sequence analysis DESCRIPTION MBCRR Software Package DESCRIPTION Calculates several different statistics on DESCRIPTION nucleic acid sequences (e.g. nucleotide, DESCRIPTION nearest neighbor, and codon boundary DESCRIPTION frequencies) for use in locating coding regions. AUTHOR - RT - ADDRESS Molecular Biology Computer Research Resource ADDRESS Dana-Farber Cancer Institute and School of Public Health ADDRESS Harvard University, 44 Binney St., Boston MA 02115 USA. CONTACT Smith T: tsmith@mbcrr.harvard.edu SITE ftp anonymous mbcrr.harvard.edu SITE Directory /MBCRR_Package SITE-CONTACT Smith T : tsmith@mbcrr.harvard.edu OS Unix LANGUAGE C VOLUME - AC BC00220 NAME CONTRAST DOMAIN Sequence analysis DESCRIPTION The program essentially calculates and then correlates the contrast DESCRIPTION vocabularies of pairs of sequences, for a certain oligomer length. DESCRIPTION The method is suitable for any linear sequences with a defined alphabet. AUTHOR Shmuel Pietrokovski RA Pietrokovski S., Hirshon J., Trifonov E.N.; RT "Linguistic measure of taxonomic and functional relatedness of RT nucleotide sequences."; RL J. Biomol. Struct. Dyn. 7:1251-1268(1990). RX Medline; 90303587. RX SeqAnalRef; PIES9001. ADDRESS Weizmann Institute of Science - Israel CONTACT Shmuel Pietrokovski SITE ftp anonymous bioinfo.weizmann.ac.il SITE Directory /pub/software/contrast SITE-CONTACT lsprilus@weizmann.weizmann.ac.il OS Unix LANGUAGE C, FORTRAN VOLUME - REQUIRES UWGCG package AC BC00221 NAME DELILA System DOMAIN Sequence analysis DESCRIPTION The Delila System is a large group of about DESCRIPTION 150 programs designed for the study of binding DESCRIPTION sites of proteins (and other things) on DNA DESCRIPTION or RNA. One of the most fun tools in the DESCRIPTION collection is called makelogo. It creates the DESCRIPTION 'sequencelogos' described in the paper by DESCRIPTION Stephens and Schneider 1990 AUTHOR Thomas Schneider toms@ncifcrf.gov RA Schneider T.D., Stormo G.D., Yarus M.A., Gold L.; RT "Delila system tools."; RL Nucleic Acids Res. 12:129-140(1984). RX Medline; 84118721. RX SeqAnalRef; SCHT8401. ADDRESS NCI/FCRDC Bldg 469. Room 144 ADDRESS P.O. Box B ADDRESS Frederick, MD 21702-1201, USA ADDRESS tel: (1 301) 846-5581 (-5532 for messages) ADDRESS fax: (1 301) 846-5598 CONTACT Tom Schneider toms@ncifcrf.gov SITE ftp anonymous ftp.ncifcrf.gov SITE Directory /pub/delila SITE-CONTACT Tom Schneider : toms@ncifcrf.gov SITE ftp anonymous ftp.bchs.uh.edu SITE Directory /pub/gene-server/unix SITE ftp anonymous ftp.bchs.uh.edu SITE Directory /pub/gene-server/vms SITE-CONTACT Dan Davison dbd@theory.bchs.uh.edu OS Unix, Vax/VMS LANGUAGE Pascal C VOLUME - AC BC00222 NAME DETECT DOMAIN Sequence analysis DESCRIPTION DETECT searches for errors that occur within coding regions DESCRIPTION of DNA sequences and that destroy the continuity of possible DESCRIPTION open reading frames. Such errors may be detected if the coded DESCRIPTION protein has a homolog within the sequence databases. In such DESCRIPTION cases translations from two different reading frames of a test DESCRIPTION sequence may have similarity runs with the correct sequence of DESCRIPTION the homolog. The similarity runs "embrace" the site of error so DESCRIPTION that the error can be localized between the end of one run and DESCRIPTION the beginning of the next run. AUTHOR Janos Posfai & Richard J. Roberts RA Posfai J., Roberts R.J.; RT "Finding errors in DNA sequences."; RL Proc. Natl. Acad. Sci. U.S.A. 89:4698-4702(1992). RX Medline; 92262507. RX SeqAnalRef; POSJ9201. ADDRESS New England Biolabs, 32 Tozer Rd.,Beverly, MA 01915. USA ADDRESS Tel: (1) 508-927-5054 CONTACT Janos Posfai or Richard J. Roberts CONTACT posfai@neb.com (roberts@neb.com) SITE ftp anonymous vent.neb.com SITE Directory /pub/software/detect SITE-CONTACT posfai@cshl.org (roberts@cshl.org) OS UNIX, Vax/VMS LANGUAGE C VOLUME - AC BC00223 NAME DM5 DOMAIN Sequence analysis AUTHOR - RT - ADDRESS University of Arizona, USA ADDRESS Genetics Software Center, Molecular & Cellular ADDRESS Biology CONTACT kmwillia@joplin.biosci.arizona.edu SITE ftp anonymous joplin.biosci.arizona.edu SITE Directory /pub/seq_analysis/dm5 SITE-CONTACT - OS IBM PC or clone, MS-DOS/PC-DOS IBM PS/2, MS- OS DOS/PC-DOS Sun-3, Unix LANGUAGE C VOLUME - AC BC00224 NAME DNA WorkBench DOMAIN Sequence analysis DESCRIPTION A program for sequence searching and manipulation DESCRIPTION Powerful and fast searches on Genbank and other databases. DESCRIPTION Client-server: access remote databases and programs DESCRIPTION Parallel distributed processing for huge databases of the near DESCRIPTION future. DESCRIPTION Many sequence manipulation functions. DESCRIPTION This list keeps growing. At present, it includes calculating DESCRIPTION the reverse complement, displaying reading frames and nucleotide DESCRIPTION to protein translations, editing, searching for restriction DESCRIPTION enzyme sites, searching for human repeat or vector in a sequence, DESCRIPTION comparing a sequence against a library or a user file, searching DESCRIPTION for a regular expression in a sequence. DESCRIPTION On my to-do list: contig assembly, searching by context-free DESCRIPTION and other grammars, feature table manipulation, GDB access, DESCRIPTION approximate regular expression matching, physical mapping of DESCRIPTION chromosomes, ... AUTHOR James Tisdall RT - ADDRESS Departments of Genetics and Computer and Information Science ADDRESS Computational Biology and Informatics Laboratory, ADDRESS Human Genome Project ADDRESS 510 Blockley Hall ADDRESS University of Pennsylvania, USA CONTACT James Tisdall tisdall@cbil.humgen.upenn.edu SITE ftp anonymous cbil.humgen.upenn.edu SITE Directory /pub/dnaworkbench SITE-CONTACT - OS Unix, Macs, and MS-DOS PCs LANGUAGE Perl language VOLUME - AC BC00225 NAME EASYMENU DOMAIN Sequence analysis DOMAIN GCG tools DESCRIPTION Provides a menu driven access to the programs DESCRIPTION contained into the Genetics Computer Group's DESCRIPTION package. AUTHOR Prilusky J. RT - ADDRESS - CONTACT - SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/vax VAX software are stored as SITE uuencoded (.UUE) files. SITE-CONTACT nethelp@ebi.ac.uk SITE ftp anonymous ftp.bchs.uh.edu (129.7.2.43)/ SITE Directory /pub/gene-server/vms SITE-CONTACT Dan Davison: dbd@theory.bchs.uh.edu OS DCL (VAX Command Language)requirements GCG 7.0 LANGUAGE C VOLUME - AC BC00226 NAME EGCG DOMAIN Sequence analysis DOMAIN GCG tools DESCRIPTION EGCG is a package of 65 programs which extend the programs DESCRIPTION in the current GCG package and add many entirely new functions. DESCRIPTION Many of the programs were previously available as "GCGEMBL" DESCRIPTION in the UNSUPPORTED.BCK saveset on the GCG distribution for VMS. DESCRIPTION As the programs are no longer entirely written at EMBL, the name DESCRIPTION of the package have changed . The "E" stands for "Extended" GCG. DESCRIPTION 26 new programs in this VMS release (* indicates programs DESCRIPTION included in the Unix release distributed by GCG on CD-ROM with DESCRIPTION GCG version 7.2) DESCRIPTION AllTrans : Translates a set of aligned DNA sequences into aligned DESCRIPTION protein sequences. DESCRIPTION *BasePairPlot : Plots the % occurrence and obs/expected frequency DESCRIPTION of any dinucleotide pair i a sequence DESCRIPTION BFastA : A version of FastA using the BLOSUM62 matrix. DESCRIPTION BTFastA : A version of TFastA using the BLOSUM62 matrix. DESCRIPTION *DbStats : Reports database statistics. DESCRIPTION *GelFigure : Produces a graphical report of a contig in a DESCRIPTION Fragment Assembly project, including restriction map, open DESCRIPTION reading frames and fragment alignment. DESCRIPTION *KabatToGcg : Converts the KABAT database to GCG format. DESCRIPTION MapSelect : Selects restriction enzymes by name or by ability to DESCRIPTION cut a specified sequence, and creates a new ENZYME.DAT file for DESCRIPTION use by other programs. DESCRIPTION *Melt : Calculates the melting temperature and %GC of a sequence. DESCRIPTION *MeltPlot : Plots the melting curve for a nucleic acid sequence. DESCRIPTION NewFeatures : An interactive editor for entering and modifying DESCRIPTION the feature table, and for minor editing of the sequence itself. DESCRIPTION Also able to understand most feature table syntax, including DESCRIPTION joins across entries and additional qualifiers. DESCRIPTION NoReturn : Removes trailing carriage returns and line feeds. DESCRIPTION *Palindrome : Searches for perfect inverted repeats. DESCRIPTION PepAllWindow : Plots hydrophobicity for one or more multiple DESCRIPTION sequence alignments. DESCRIPTION PepCoil : Identifies potential coiled-coil regions in proteins. DESCRIPTION *PlotAlign : Plots conserved properties at each position in a DESCRIPTION multiple sequence alignment. DESCRIPTION *SeqDbToGcg : Converts the SEQDB database to GCG format. DESCRIPTION ToEmbl : Extracts an EMBL entry in EMBL format. DESCRIPTION ToGenBank : Extracts a GenBank entry in GenBank format. DESCRIPTION ToPirAll : Converts a set of sequences of subsequences into a DESCRIPTION single file in PIR format. DESCRIPTION *ToText : Converts a sequence to plain text. DESCRIPTION TProfileGap : ProfileGap with optional 6-frame translation of a DESCRIPTION DNA sequence. DESCRIPTION TProfileSearch : ProfileSearch with ability to search any size of DESCRIPTION database, and optional 6-frame translation of DNA databases. DESCRIPTION TProfileSegments : [1,2] Processes the output file from DESCRIPTION TProfileSearch. DESCRIPTION TSegments : Processes TWordSearch output. DESCRIPTION TWordSearch : WordSearch with a 6-frame translation of the DESCRIPTION database. DESCRIPTION 19 GCG programs with command line control DESCRIPTION Command line control has been added to all the GCG programs that DESCRIPTION did not provide full support. This work was done by summer DESCRIPTION student Jaakko Hattula from Tampere University of Technology in DESCRIPTION Finland. The programs (see the GCG manual for details) are: DESCRIPTION EAssemble, ECodonFrequency, ECompTable, EConsensus, ECorrespond, DESCRIPTION ECrypt, EDiverge, EExtractPeptide, EFingerPrint, EFromStaden, DESCRIPTION EGetSeq, EPublish, ERepeat, EReverse, EStatPlot, ETerminator, DESCRIPTION EToStaden, ETranslate, EWindow DESCRIPTION 20 programs from the original GCGEMBL package, many now enhanced: DESCRIPTION Antigenic : Reports potential antigenic regions. DESCRIPTION CheckLen : Calculates checksums for entries in a database. DESCRIPTION CheckLenComp : Compares CheckLen output for two databases, and DESCRIPTION reports a list of unique entries. DESCRIPTION CpGPlot : Plots the frequency of occurrence of CG dinucleotides DESCRIPTION and percentage of C and G in a sequence. DESCRIPTION FastACheck : Selects significant alignments from (T)Fasta output DESCRIPTION files. DESCRIPTION GbOnly : Creates a list of GenBank entries that have accession DESCRIPTION numbers not found in the latest EMBL release. DESCRIPTION GelAnalyze : Reads the output of GelStatus, and produces project DESCRIPTION statistics for shotgun sequencing. DESCRIPTION GelPicture : Displays a diagram and printout of a contig from a DESCRIPTION Fragment Assembly project, with ambiguities highlighted. DESCRIPTION GelStatus : Reports progress of a Fragment Assembly project. DESCRIPTION HelixTurnHelix : Predicts helix-turn-helix DNA binding domains. DESCRIPTION NewQuickIndex : A much faster version of QuickIndex that produces DESCRIPTION the index files for NewQuickSearch. DESCRIPTION NewQuickSearch : A much faster version of QuickSearch that can DESCRIPTION run on almost all systems without a major virtual memory DESCRIPTION overhead. DESCRIPTION PepNet : Displays part of a protein as a helical net. DESCRIPTION PepStats : Gives a short statistical summary on the composition DESCRIPTION of a protein sequence, or a 3-franme translation. DESCRIPTION PepWheel : Displays part of a protein as a helical wheel. DESCRIPTION PepWindow : Plots hydrophobicity of a protein sequence. DESCRIPTION PirOnly : Selects entries from PIR that are not in the latest DESCRIPTION Swiss-Prot release. DESCRIPTION PrettyPlot : Displays multiple sequence alignments with boxes DESCRIPTION around conserved regions. DESCRIPTION QuickMatch : Displays the overlaps found by NewQuickSearch DESCRIPTION (or by QuickSearch), with selection for good quality matches. DESCRIPTION SigCleave : Predicts signal peptide cleavage sites. AUTHOR Version 7.2 of the EGCG Programs was prepared by AUTHOR Peter Rice (EMBL, Heidelberg, Germany), Rodrigo Lopez AUTHOR (Biotechnology Centre of Oslo, Norway), Jaakko Hattula AUTHOR (Tampere University of Technology, Finland),Reinhard Doelz AUTHOR (Basel, Switzerland) and Jack Leunissen (CAOS/CAMM Centre, AUTHOR Netherlands). RA Gibson T.J., Rice P.M., Thompson J.D., Heringa J.; RT "KH domains within the FMR1 sequence suggest that RT fragile X syndrome stems from a defect in RNA metabolism."; RL Trends Biochem. Sci. 18:331-333(1993). RX Medline; 94054651. RA Musacchio A., Gibson T., Rice P., Thompson J., Saraste M.; RT "The PH domain: a common piece in the structural RT patchwork of signalling proteins."; RL Trends Biochem. Sci. 18:343-348(1993). RX Medline; 94054654. ADDRESS - CONTACT Peter Rice Peter.Rice@sanger.ac.uk CONTACT Rodrigo Lopez rodrigol@biotek.uio.no SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/vax/egcg SITE by E-mail from the EMBL Network File Server SITE Send E-mail to address NETSERV@ebi.ac.uk with the SITE following message text: SITE HELP SOFTWARE SITE HELP VAX_SOFTWARE SITE GET VAX_SOFTWARE:EGCG.UAA SITE-CONTACT - OS Porting of the EGCG programs from VAX/VMS to ALPHA OpenVMS was OS supported by DEC under a University Porting Agreement. LANGUAGE - VOLUME - AC BC00227 NAME EXTRACT DOMAIN Sequence analysis DESCRIPTION MBCRR Software Package DESCRIPTION Creates sub-libraries from IntelliGenetics- DESCRIPTION formatted sequence files with options to DESCRIPTION translate nucleic acid sequences and to extract DESCRIPTION sequence sub-regions. AUTHOR - RT - ADDRESS Molecular Biology Computer Research Resource ADDRESS Dana-Farber Cancer Institute and School of Public Health ADDRESS Harvard University, 44 Binney St., Boston MA 02115 USA. CONTACT Smith T: tsmith@mbcrr.harvard.edu SITE ftp anonymous mbcrr.harvard.edu SITE Directory /MBCRR_Package SITE-CONTACT Smith T tsmith@mbcrr.harvard.edu OS Unix LANGUAGE C VOLUME - AC BC00228 NAME FALCON DOMAIN Sequence analysis DOMAIN Contig assembly software DESCRIPTION Fast Assembly of Large CONtig, is a program for shotgun DESCRIPTION DNA sequence assembly DESCRIPTION It can handle genome-size projects (it has assembled 12 megabases DESCRIPTION of raw test data into a single 3 megabase DESCRIPTION consensus of approximately 30,000 fragments in 10.2 hours DESCRIPTION on a DEC OSF/1 ALPHA). Larger projects should simply be DESCRIPTION matter of adding additional virtual memory. AUTHOR Gary P. Gryan (gryan@rascal.med.harvard.edu) RT - ADDRESS Harvard Medical School, Department of Genetics, ADDRESS Howard Hughes Medical Institute, 200 Longwood Avenue, ADDRESS Boston, MA 02115, USA CONTACT gryan@rascal.med.harvard.edu SITE ftp anonymous rascal.med.harvard.edu SITE Directory /gryan/falcon SITE-CONTACT - OS Unix (DEC ALPHA running OSF/1 v1.3 DEC C compiler) OS ULTRIX (DECSTATION 5000 running Ultrix 4.3) OS VMS (VAX 4000/90 running VAX/VMS 5.5-2 using VAX C compiler) LANGUAGE ANSI C VOLUME - REQUIRES - COMMENTS If you wish to be informed of updates, get tech-notes, COMMENTS and receive announcement of further developments of this program, COMMENTS send e-mail to gryan@rascal.med.harvard.edu AC BC00229 NAME GCGDBASE DOMAIN Sequence analysis DOMAIN GCG tools DESCRIPTION GCG extensions developed at EMBL for using new DESCRIPTION EMBL distribution format AUTHOR Rice P. RT - ADDRESS - CONTACT - SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/vax VAX software are stored as SITE uuencoded (.UUE) files. SITE-CONTACT nethelp@ebi.ac.uk SITE ftp anonymous ftp.bchs.uh.edu (129.7.2.43)/ SITE Directory /pub/gene-server/vms SITE-CONTACT Dan Davison: dbd@theory.bchs.uh.edu OS - LANGUAGE FORTRAN C VOLUME - REQUIRES GCG package v6 AC BC00230 NAME GCGEMBL DOMAIN Sequence analysis DOMAIN GCG tools DESCRIPTION GCG extensions developed at EMBL AUTHOR Rice P. RT - ADDRESS - CONTACT - SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/vax VAX software are stored as SITE uuencoded (.UUE) files. SITE-CONTACT nethelp@ebi.ac.uk SITE ftp anonymous ftp.bchs.uh.edu (129.7.2.43)/ SITE Directory /pub/gene-server/vms SITE-CONTACT Dan Davison: dbd@theory.bchs.uh.edu OS - LANGUAGE FORTRAN C VOLUME - REQUIRES GCG package v6 AC BC00231 NAME GCGMENU DOMAIN Sequence analysis DOMAIN GCG tools DESCRIPTION Extendable menu interface to GCG package AUTHOR Gartmann, C. RA Gartmann C.J., Grob U.; RT "A menu-shell for the GCG programs."; RT Comput. Appl. Biosci. 7:457-460(1991). RX Medline; 92083354. RX SeqAnalRef; GARC9101. ADDRESS Max-Planck-Institut fur Immunbiologie, Freiburg, FRG. CONTACT - SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/vax VAX software are stored as SITE uuencoded (.UUE) files. SITE-CONTACT nethelp@ebi.ac.uk OS - LANGUAGE FORTRAN C VOLUME - REQUIRES GCG package v7.0 AC BC00232 NAME GCGQUICK DOMAIN Sequence analysis DOMAIN GCG tools DESCRIPTION GCG extensions developed at EMBL for speeding DESCRIPTION up QuickSearch AUTHOR Rice P. RT - ADDRESS - CONTACT - SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/vax VAX software are stored as SITE uuencoded (.UUE) files. SITE-CONTACT nethelp@ebi.ac.uk SITE ftp anonymous ftp.bchs.uh.edu (129.7.2.43)/ SITE Directory /pub/gene-server/vms SITE-CONTACT Dan Davison: dbd@theory.bchs.uh.edu OS - LANGUAGE FORTRAN C VOLUME - REQUIRES GCG package v6 AC BC00233 NAME GCGSHELLS1 DOMAIN Sequence analysis DOMAIN GCG tools DESCRIPTION DCL shells for many GCG programs AUTHOR Clark S. RT - ADDRESS - CONTACT - SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/vax VAX software are stored as SITE uuencoded (.UUE) files. SITE-CONTACT nethelp@ebi.ac.uk SITE ftp anonymous ftp.bchs.uh.edu (129.7.2.43)/ SITE Directory /pub/gene-server/vms SITE-CONTACT Dan Davison: dbd@theory.bchs.uh.edu OS DCL, requirements : VAX Fortran LANGUAGE FORTRAN C VOLUME - AC BC00234 NAME GCGSHELLS2 DOMAIN Sequence analysis DOMAIN GCG tools DESCRIPTION DCL shells to facilitate GenBank on-line DESCRIPTION service access AUTHOR Clark S. RT - ADDRESS - CONTACT - SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/vax VAX software are stored as SITE uuencoded (.UUE) files. SITE-CONTACT nethelp@ebi.ac.uk SITE ftp anonymous ftp.bchs.uh.edu (129.7.2.43)/ SITE Directory /pub/gene-server/vms SITE-CONTACT Dan Davison: dbd@theory.bchs.uh.edu OS VAX/VMS LANGUAGE DCL, VAX FORTRAN C VOLUME - AC BC00235 NAME GCG Wisconsin Package DOMAIN Sequence analysis DOMAIN GCG tools DESCRIPTION Editing , Fragment Assembly , Mapping DESCRIPTION Comparison , Sequence Database Searching , DESCRIPTION Multiple Sequence Analysis , DESCRIPTION Pattern Recognition , RNA Secondary Structure DESCRIPTION Protein Analysis , Translation , Manipulation DESCRIPTION Display , Sequence Exchange File Utilities AUTHOR - RT - ADDRESS Genetics Computer Group, USA ADDRESS 575 Science Drive, Madison, Wisconsin 53711 U.S.A. DDRESS Tel: 1-608-231-5200. Fax: 1-608-231-5202. CONTACT Dina A. Beers (Customer Relations) : Beers@gcg.com CONTACT help@gcg.com OS VAX or AXP with OpenVMS 6.1, AXP (RISC) with OSF/1 2.0, OS IBM (RISC) with AIX 3.2.5, SGI (RISC) with Irix 5.2, OS Sun (Sparc) with Solaris 2.3 LANGUAGE Fortran, C VOLUME - AC BC00237 NAME GDE DOMAIN Sequence analysis DOMAIN Alignment editing and display DESCRIPTION Genetic Data Environement DESCRIPTION Ensemble de programmes d' analyse de sequences DESCRIPTION assemblage de contigs,recherches de DESCRIPTION similarites , analyses phylogenetiques AUTHOR Steven Smith AUTHOR S.W. Smith, R. Overbeek,C.R. Woese, W. Gilbert and P.M. Gillevet RA Smith S.W., Overbeek R., Woese C.R., Gilbert W., Gillevet P.M.; RT "The Genetic data environment and expandable GUI for multiple RT sequence analysis."; RT Comput. Appl. Biosci. 10(6):671-675(1994). RX SeqAnalRef; SMIS9401. ADDRESS - CONTACT Tim Littlejohn tim@bch.umontreal.ca SITE ftp anonymous megasun.BCH.UMontreal.CA Official SITE SITE Directory /pub SITE-CONTACT Tim Littlejohn tim@bch.umontreal.ca SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/unix UNIX software are stored SITE as archive (tar) files compressed (.Z). SITE-CONTACT nethelp@ebi.ac.uk SITE ftp anonymous ftp.bchs.uh.edu (129.7.2.43) SITE Directory /pub/gene-server/unix SITE-CONTACT Dan Davison: dbd@theory.bchs.uh.edu OS SUN Sparc-station (portage sur SGI, OS DECStation, Cray)system Unix, SunOS 4.1, OS OpenWindows 2.0 or MIT X11R4 LANGUAGE C VOLUME - COMMENTS Menu items for GDE are now available for the following programs COMMENTS from the FSAP package: COMMENTS NUMSEQ - sequence numbering, formatting & translation COMMENTS BACHREST - batch restriction site search. Now uses REBASE. COMMENTS P1HOM, - dot-matrix similarity searches for DNA and protein COMMENTS P2HOM,D3HOM,D4HOM COMMENTS These files are included in the file fsap.tar.Z in the directory COMMENTS psgendb at ftp.cc.umanitoba.ca. AC BC00238 NAME GENETYX DOMAIN Sequence analysis DESCRIPTION Nucleic acid and protein analysis AUTHOR Stoevlbaek J. RT - ADDRESS Software Development Co., Ltd. CONTACT Biotechnology Div. SITE - SITE-CONTACT - OS Sun-3, Sun-4, Unix LANGUAGE - VOLUME - AC BC00239 NAME GENINFO SOFTWARE TOOLBOX DOMAIN Sequence analysis DESCRIPTION The GenInfo Software Toolbox is a set of DESCRIPTION software and data exchange specifications that DESCRIPTION are used by NCBI to produce portable, modular DESCRIPTION software for molecular biology. DESCRIPTION api Application Programmer Interface, DESCRIPTION Sequence Utilities DESCRIPTION asn ASN.1 specifications for publications DESCRIPTION and sequences asnlib Source code for AsnLib and DESCRIPTION asntool asnload AsnLib headers and dynamic DESCRIPTION parse tables (Mac and PC) DESCRIPTION asnstat AsnLib headers that use static memory DESCRIPTION (UNIX and VMS) DESCRIPTION bin Asntool executable copied here DESCRIPTION browser Source code for Entrez application DESCRIPTION build Empty directory for building tools DESCRIPTION and libraries DESCRIPTION cdromlib Access routines for data on the DESCRIPTION Entrez CD-ROM DESCRIPTION cdrom06 Files for compatibility with Entrez DESCRIPTION pre-release 6 DESCRIPTION config Configuration files for NCBI software DESCRIPTION corelib Source code for NCBI Core Software DESCRIPTION Library DESCRIPTION data Data files used for sequence DESCRIPTION conversion DESCRIPTION demo AsnLib and sequence utility DESCRIPTION demonstration programs DESCRIPTION doc Documentation in ASCII files DESCRIPTION include Include files required by DESCRIPTION applications are copied here DESCRIPTION lib Libraries copied here DESCRIPTION macmpw Files for compiling with Macintosh MPWC DESCRIPTION make Make files for various systems DESCRIPTION msdos Files for compiling with Microsoft C DESCRIPTION for DOS DESCRIPTION mswin Files for compiling with Microsoft C DESCRIPTION and Windows DESCRIPTION object Functions for reading and writing DESCRIPTION complex objects DESCRIPTION readme File that contains important building DESCRIPTION instructions DESCRIPTION vibrant Source code for Vibrant portable DESCRIPTION interface package AUTHOR NCBI RT - ADDRESS National Center for Biotechnology Information ADDRESS National Library of Medicine, Bldg. 38A, Room 8N-811 ADDRESS Bethesda, MD 20894, USA. CONTACT - SITE ftp anonymous ncbi.nlm.nih.gov SITE Directory /toolbox SITE-CONTACT Scott Federhen: info@ncbi.nlm.nih.gov SITE ftp anonymous ftp.bio.indiana.edu SITE Directory /molbio/ncbi SITE-CONTACT Don Gilbert : gilbertd@cricket.bio.indiana.edu OS - LANGUAGE - VOLUME - AC BC00240 NAME GENPROD DOMAIN Sequence analysis DESCRIPTION takes as input a file of nucleic-acid sequence entries in DESCRIPTION genbank format and outputs a file of amino-acid sequence entries DESCRIPTION in a format similar to genbank. The nucleic-acid entries are DESCRIPTION translated using Fickett's pepttr program based on extracting DESCRIPTION pept features. AUTHOR - RT - ADDRESS - CONTACT IntelliGenetics, Inc SITE ftp anonymous turbo.bio.net SITE Directory /pub/unix SITE-CONTACT - OS Unix LANGUAGE - VOLUME - AC BC00241 NAME GGREP DOMAIN Sequence analysis DESCRIPTION MBCRR Software Package DESCRIPTION Performs "regular expression" pattern DESCRIPTION searches of nucleic acid or protein sequences DESCRIPTION (including entire sequence databases) using DESCRIPTION the GNU-Emacs regular expression handler. AUTHOR Temple Smith RT - ADDRESS Molecular Biology Computer Research Resource ADDRESS Dana-Farber Cancer Institute and School of Public Health ADDRESS Harvard University, 44 Binney St., Boston MA 02115 USA. CONTACT Smith T: tsmith@mbcrr.harvard.edu SITE ftp anonymous mbcrr.harvard.edu SITE Directory /MBCRR-Package SITE-CONTACT Smith T: tsmith@mbcrr.harvard.edu OS Unix LANGUAGE C VOLUME - AC BC00242 NAME GM DOMAIN Sequence analysis DESCRIPTION Analysis of unknown DNA sequences AUTHOR Fields C.A. and Soderlund C.A. RA Fields C.A., Soderlund C.A.; RT "gm: a practical tool for automating DNA sequence analysis."; RL Comput. Appl. Biosci. 6:263-270(1990). RX Medline; 91003520. RX SeqAnalRef; FIEC9001. ADDRESS Computing Research Laboratory, New Mexico State University, ADDRESS Las Cruces 88003-0001, USA. CONTACT - SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/unix UNIX software are stored SITE as archive (tar) files compressed (.Z). SITE-CONTACT nethelp@ebi.ac.uk SITE ftp anonymous ftp.bchs.uh.edu (129.7.2.43)/ SITE Directory /pub/gene-server/unix SITE-CONTACT Dan Davison: dbd@theory.bchs.uh.edu OS - LANGUAGE - VOLUME - AC BC00243 NAME ICATOOLS DOMAIN Sequence analysis DESCRIPTION Clustering and statistical analysis of large DESCRIPTION cDNA collections, grouping sequences together on DESCRIPTION the basis of local sequence similarity. DESCRIPTION The first set of programs is composed by : DESCRIPTION ICAtool, ICAprint and ICAstats (descr in [1]). DESCRIPTION A new set of tools is described in [2] and is DESCRIPTION composed by ICAass, N2tool and ICAmatches. AUTHOR Parsons J. RA Parsons J.D., Brenner S., Bishop M.J.; RT "Clustering cDNA sequences."; RT Comput. Appl. Biosci. 8:461-466(1992). RX Medline; 93045593. RX SeqAnalRef; PARS9201. RA Parsons J.D.; RT "Improved tools for DNA comparison and clustering."; RL Comput. Appl. Biosci. 11(6):603-613(1995). ADDRESS Genome Sequencing Center, Washington University School of ADDRESS Medecine, 4444 Forest Park Avenue, St Louis, MO 63108, USA CONTACT jparsons@watson.wutsl.edu SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/unix UNIX software are stored SITE as archive (tar) files compressed (.Z). SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/vax VAX software are stored as SITE uuencoded (.UUE) files. SITE-CONTACT nethelp@ebi.ac.uk OS Unix Vax/VMS LANGUAGE C VOLUME - AC BC00244 NAME IG SUITE DOMAIN Sequence analysis DESCRIPTION Nucleic acid and protein analysis of all types AUTHOR - RT - ADDRESS IntelliGenetics Inc CONTACT Dave Callender, Director of Sales and Customer CONTACT Service SITE - SITE-CONTACT - OS Sun-3 and Sun-4, Unix, SPARC Stations, VAX, VMS LANGUAGE C VOLUME - AC BC00245 NAME MENUGCG DOMAIN Sequence analysis DOMAIN GCG tools DESCRIPTION Menu interface to GCG package AUTHOR Marc Colet RT - ADDRESS BEN ADDRESS Rue des Chevaux 67, 1640 Rhode-Saint-Genese, BELGIUM CONTACT mcolet@dbm.ulb.ac.be SITE ftp anonymous ftp.be.embnet.org SITE Directory /pub/menugcg SITE as archive (tar) files compressed (.Z). SITE-CONTACT gbottu@dbm.ulb.ac.be OS Unix LANGUAGE csh script VOLUME - REQUIRES GCG v8 or 9 AC BC00246 NAME MOLBIO++ DOMAIN Sequence analysis DESCRIPTION molbio++ is a C++ library for molecular biosequence analysis. DESCRIPTION Major features include: DESCRIPTION classes and services for reading and writing sequence data in DESCRIPTION the following formats: Genbank Flatfile , EMBL / SwissProt DESCRIPTION GCG / Wisconsin , Fasta / Pearson , PIR , NCBI Retrieve Server DESCRIPTION (read-only) DESCRIPTION limited parsing of fields and features in biosequence files DESCRIPTION storing amino acid or nucleic acid sequences iterating over DESCRIPTION a biosequence DESCRIPTION calculating and storing counts or frequencies of amino acids DESCRIPTION or nucleotides DESCRIPTION device-independent graphics, via GCG's FIGURE program DESCRIPTION translating nucleotide sequences into proteins using DESCRIPTION the universal genetic code or modifications thereof. DESCRIPTION parsing BLAST output DESCRIPTION calculating pI and molecular weight of proteins amino acid DESCRIPTION hydropathy values of Kyte & Doolittle AUTHOR Keith Robison RT - ADDRESS Harvard University Department of Cellular and Developmental ADDRESS Biology Department of Genetics (Harvard Medical School) / HHMI CONTACT Keith Robison: robison@biosun.harvard.edu SITE ftp anonymous golgi.harvard.edu SITE Directory /pub/robison SITE-CONTACT - SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/unix UNIX software are stored SITE as archive (tar) files compressed (.Z). SITE-CONTACT nethelp@ebi.ac.uk OS Sparcstation LANGUAGE C ++ VOLUME - AC BC00247 NAME NCBI DOMAIN Sequence analysis DESCRIPTION General purpose routines used by BLAST AUTHOR Gish W. RA Altschul S.F., Gish W., Miller W., Myers E.W., Lipman D.J.; RT "Basic local alignment search tool."; RL J. Mol. Biol. 215:403-410(1990). RX Medline; 91039304. RX SeqAnalRef; ALTS9002. ADDRESS National Center for Biotechnology Information ADDRESS National Library of Medicine, Bldg. 38A, Room 8N-811 ADDRESS Bethesda, MD 20894, USA. CONTACT - SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/unix UNIX software are stored SITE as archive (tar) files compressed (.Z). SITE-CONTACT nethelp@ebi.ac.uk OS C LANGUAGE C VOLUME - AC BC00248 NAME ORF DOMAIN Sequence analysis DESCRIPTION module to extract all orfs from a nucleotide DESCRIPTION sequence within a given range, default is 60 DESCRIPTION nt to 10000 nt AUTHOR Jean Michel Claverie RT Computers and Chemistry (in press) ADDRESS National Center for Biotechnology Information ADDRESS National Library of Medicine, Bldg. 38A, Room 8N-811 ADDRESS Bethesda, MD 20894, USA. CONTACT jmc@ncbi.nlm.nih.gov SITE ftp anonymous ncbi.nlm.nih.gov SITE Directory /pub/jmc SITE-CONTACT info@ncbi.nlm.nih.gov OS Unix LANGUAGE C VOLUME - AC BC00249 NAME QC DOMAIN Sequence analysis DOMAIN Statistical significance DESCRIPTION The qc program calculates the hexanucleotide frequences or any DESCRIPTION other n from 2-x in dna from separate groups and then does a DESCRIPTION liklihood ratio test on the maximum liklihood under the binomial DESCRIPTION model that the two samples are the same or different using a DESCRIPTION chi-square statistic. AUTHOR Owen White (owhite@tigr.org), Ted Dunning (ted@nmsu.edu) RA White O., Dunning T.; RT "Accurate methods for the statistics of surprise and RT coincidence."; RL in press (?). RA White O., Dunning T., Sutton G., Adams M., Venrer J.C., Field C.; RT "A quality control algorithm for DNA sequencing projects."; RL Nucleic Acids Res. 21:3829-3838(1993). RX Medline; 93376509. RX SeqAnalRef; WHIO9301. ADDRESS The Institute for Genomic Research ADDRESS 932 Clopper Road ADDRESS Gaithersburg, MD 20878, USA CONTACT - SITE ftp anonymous ftp.tigr.org SITE Directory /pub/qc SITE-CONTACT - OS Unix LANGUAGE C, flex VOLUME - REQUIRES the lexical interpreter 'flex' from GNU COMMENTS GNU flex bcan be found at prep.ai.mit.edu Directory /pub/gnu AC BC00250 NAME SEQCOMP DOMAIN Sequence analysis DESCRIPTION Analysis of peptide composition in a protein DESCRIPTION sequence AUTHOR Dessen P. RA Dessen P., Fondrat C., Valencien C., Mugnier C.; RT "BISANCE: A French service for access to biomolecular RT sequence databases."; RL Comput. Appl. Biosci. 6:355-356(1990). RX Medline; 91077760. RX SeqAnalRef; DESP9001. ADDRESS - CONTACT - SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/vax VAX software are stored as SITE uuencoded (.UUE) files. SITE-CONTACT nethelp@ebi.ac.uk OS - LANGUAGE FORTRAN VOLUME - AC BC00251 NAME SEQSEE DOMAIN Sequence analysis DESCRIPTION General purpose sequence analysis DESCRIPTION SEQSEE (SEQuence SEEker) is a multi-purpose, menu-driven DESCRIPTION suite of programs designed to provide a fully integrated, DESCRIPTION state-of-the-art package for the analysis and display of DESCRIPTION protein sequences and protein databases. It is currently DESCRIPTION configured to run on most UNIX-based machines including DESCRIPTION Sun, SGI and NeXT workstations with conversion to other DESCRIPTION architectures (e.g. Vax or Cray) being a relatively simple DESCRIPTION task. SEQSEE is capable of performing nearly all of the DESCRIPTION analytical and comparative tasks found in most DESCRIPTION comprehensive commercially available software packages. DESCRIPTION These include sequence/database searching, sequence DESCRIPTION retrieval, sequence entry and editing, statistical sequence DESCRIPTION analysis, multiple sequence alignment, flexible pattern DESCRIPTION matching, and secondary structure prediction. SEQSEE also DESCRIPTION integrates a number of unique databases which allow it to DESCRIPTION perform many additional functions such as structure-based DESCRIPTION sequence alignments and homology-based secondary structure DESCRIPTION prediction. Additional enhancements to many previously DESCRIPTION published algorithms have substantially improved the DESCRIPTION performance of SEQSEE over that found for most other DESCRIPTION commercial products. AUTHOR - RA Wishart D.S., Boyko R.F., Willard L., Richards F.M., Sykes B.D.; RT "SEQSEE: a comprehensive program suite for protein sequence analysis."; RL Comput. Appl. Biosci. 10:121-132(1994). RX Medline; 94290907. RX SeqAnalRef; WISD9401. ADDRESS SEQSEE c/o PENCE ADDRESS 7-13 HMRC ADDRESS University of Alberta, Edmonton, AB T6G 2S2, Canada ADDRESS Fax: (1) 403 492-1473 CONTACT seqsee@procyon.biochem.ualberta.ca SITE ftp anonymous canopus.biochem.ualberta.ca SITE Directory /pub/ SITE-CONTACT - OS Unix (SUN and SGI) LANGUAGE - VOLUME - REQUIRES - AC BC00252 NAME SIGNAL DOMAIN Sequence analysis DESCRIPTION This program implements the Von Heijne algorithm to find DESCRIPTION potential signal sequences (reference is at the end of the code). DESCRIPTION It does a very good job at finding real signals, even internal DESCRIPTION and atypical signals. used to: DESCRIPTION -provide evidence that some newly cloned gene encode a DESCRIPTION secreted protein DESCRIPTION -identify weak of unusual internal signal sequences DESCRIPTION -identify mutations that would likely affect secretion DESCRIPTION -examine the statistical distribution of signal sequences in DESCRIPTION real protein sequences and in random sequences. AUTHOR Robert C. Colgrove RT Colgrove, RC, PhD Dissertation, UCSF dept of Biochemistry, 1990. ADDRESS - CONTACT RC Colgrove colgrove@xtal10.harvard.edu SITE - SITE-CONTACT - OS UNIX LANGUAGE C VOLUME - AC BC00253 NAME SIGNAL SCAN DOMAIN Sequence analysis DESCRIPTION SIGNAL SCAN is a program developed to DESCRIPTION facilitate the analysis of DNA sequences for DESCRIPTION known eukaryotic signals. AUTHOR Prestridge, D.S. RA Prestridge D.S.; RT "SIGNAL SCAN: a computer program that scans DNA sequences for RT eukaryotic transcriptional elements."; RL Comput. Appl. Biosci. 7:203-206(1991). RX Medline; 91283895. RX SeqAnalRef; PRED9101. RA Prestridge D.S., Stormo G.D.; RT "SIGNAL SCAN 3.0: new database and program features."; RL Comput. Appl. Biosci. 9:113-115(1993). RX Medline; 93169491. RX SeqAnalRef; PRED9301. ADDRESS Director, Advanced Biosciences Computing Center ADDRESS University of Minnesota, USA CONTACT danp@biosci.cbs.umn.edu SITE ftp anonymous ftp.bio.indiana.edu SITE Directory /molbio/search SITE-CONTACT D Gilbert: gilbertd@cricket.bio.indiana.edu SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/vax (sscan) VAX software are SITE stored as uuencoded (.UUE) files. SITE-CONTACT nethelp@ebi.ac.uk SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/unix/signalscan SITE-CONTACT nethelp@ebi.ac.uk SITE ftp anonymous ftp.bchs.uh.edu stored as SITE sscan.uua and sscan.uub SITE Directory /pub/gene-server/unix SITE-CONTACT Dan Davison: dbd@theory.bchs.uh.edu OS Unix, VMS LANGUAGE - VOLUME - AC BC00254 NAME Matrix Search DOMAIN Sequence analysis DOMAIN Database and analysis DOMAIN Searching databases DESCRIPTION Matrix Search is a program that finds potential transcription DESCRIPTION factor binding sites in DNA sequences using IMD, a database DESCRIPTION of matrices of transcription factors. It allows the user to DESCRIPTION search an input sequence with IMD, to visualize the matrix DESCRIPTION representation of a site, and to retrive journal citations DESCRIPTION about each factor. It can be obtained by anonymous ftp to: AUTHOR Qing K.Chen, Gerald Z. Hertz, and Gary D. Stormo RA Chen Q.K., Hertz G.Z., Stormo D.G.; RT "MATRIX SEARCH 1.0: a computer program that scans DNA sequences RT for transcriptional elements using a database of weight matrices."; RL Comput. Appl. Biosci. 11(5):563-566(1995). ADDRESS Department of Molecular, Cellular, and Developmental Biology ADDRESS University of Colorado at Boudler ADDRESS Boulder, CO 80309-0347 CONTACT chenq@beagle.colorado.edu SITE ftp anonymous beagle.colorado.edu SITE Directory /pub SITE get file imd.tar SITE-CONTACT putz@beagle.colorado.edu OS Unix systems LANGUAGE C VOLUME 1.5M REQUIRES - COMMENTS Matrix Search and IMD is also incorparated into the program COMMENTS Signal Scan 4.0 by Dr. Dan Prestridge(danp@molbio.umn.edu AC BC00255 NAME SIGSEQ DOMAIN Sequence analysis DESCRIPTION Prediction of signal sequence cleavage site DESCRIPTION SIGSEQ predicts the most likely cleavage site in a signal DESCRIPTION peptide sequence, based on the rules and probability tables DESCRIPTION described in G. von Heijne, Nucleic Acid Res. 14:4683(1986). DESCRIPTION The prediction is based on a scanning the sequence DESCRIPTION using a window of length 15, starting from the N-terminus. The DESCRIPTION probability of a particular window containing the actual DESCRIPTION cleavage site is derived from values given each amino acid DESCRIPTION according to type and position in the window. The cleavage site DESCRIPTION is defined as between position 13 and 14 (-1,+1 position). AUTHOR Anthony Popowicz and Patricia Dash RA Popowicz A.M., Dash P.F.; RT "SIGSEQ: a computer program for predicting signal sequence RT cleavage sites."; RL Comput. Appl. Biosci. 4:405-406(1988). RX Medline; 88327418. RX SeqAnalRef; POPA8801. RA von Heijne G.; RT "A new method for predicting signal sequence cleavage sites."; RL Nucleic Acid Res. 14:4683-4690(1986). RX Medline; 86232600. ADDRESS Rockefeller University, Computing Services, New York, NY 10021. CONTACT - SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/unix UNIX software are stored SITE as archive (tar) files compressed (.Z). SITE-CONTACT nethelp@ebi.ac.uk SITE ftp anonymous ftp.bchs.uh.edu (129.7.2.43)/ SITE Directory /pub/gene-server/unix SITE-CONTACT Dan Davison: dbd@theory.bchs.uh.edu OS Unix LANGUAGE C VOLUME - AC BC00256 NAME SINCAIDEN DOMAIN Sequence analysis DESCRIPTION Sequences analysis AUTHOR - RT - ADDRESS - CONTACT Fujitsu Ltd National Institute of genetics, CONTACT Japan SITE - SITE-CONTACT - OS SunOS 4.0.3 Sun , Fujitsu S/4 LANGUAGE - VOLUME - AC BC00257 NAME SQUIRREL DOMAIN Sequence analysis DOMAIN GCG tools DESCRIPTION SQUIRREL is a set of programs to analyze signal regions in DNA DESCRIPTION sequences. The method is based on sequence consensus matrices. DESCRIPTION A signal is composed of several signal blocks separated from DESCRIPTION each other by variable distances. DESCRIPTION Programs are provided to align and create block matrices and DESCRIPTION to search for signals in larger sequences. DESCRIPTION The programs provide a full-screen user-interface with online DESCRIPTION help. DESCRIPTION GCG, although not necessary, is highly recommended. AUTHOR Ch. Gartmann & U. Grob RA Gartmann C.J., Grob U.; RT "SQUIRREL: Sequence QUery, Information Retrieval and REporting RT Library. A program package for analyzing signals in nucleic RT acid sequences for the VAX."; RL Nucleic Acids Res. 19(21):6033-6040(1991). RX Medline; 92051397. RX SeqAnalRef; GARC9102. ADDRESS Christoph Gartmann, Max-Planck-Institut fuer Immunbiologie ADDRESS Freiburg, FRG CONTACT gartmann@immunbio.mpg.de SITE - SITE-CONTACT - OS VAX - VMS LANGUAGE Pascal VOLUME - AC BC00258 NAME STADEN DOMAIN Contig assembly software DOMAIN Sequence analysis DESCRIPTION Staden Package Automated Sequence Input, Editing DESCRIPTION and Analysis AUTHOR Staden R. RA Dear S., Staden R.; RT "A sequence assembly and editing program for efficient management RT of large projects."; RL Nucleic Acids Res. 19:3907-3911(1991). RX Medline; 91319550. RX SeqAnalRef; DEAS9101. RT "A standard file format for data from DNA sequencing RT instruments."; RL DNA Seq. 3:107-110(1992). RX Medline; 93091241. RX SeqAnalRef; DEAS9301. RA Staden R.; RT "Finding protein coding regions in genomic sequences."; RL Meth. Enzymol. 183:163-180(1990). RX Medline; 90190365. RX SeqAnalRef; STAR9001. RA Staden R.; RT "Searching for patterns in protein and nucleic acid sequences."; RL Meth. Enzymol. 183:193-211(1990). RX Medline; 90190367. RX SeqAnalRef; STAR9002. RA Staden R.; RT "Screening protein and nucleic acid sequences against libraries RT of patterns."; RL DNA Seq. 1:369-374(1991). RX Medline; 92119325. RX SeqAnalRef; STAR9101. RA Staden R., Dear S.; RT "Indexing the sequence libraries: software providing a common RT indexing system for all the standard sequence libraries."; RL DNA Seq. 3:99-105(1992). RX Medline; 93091251. RX SeqAnalRef; STAR9201. RA Dear, S. and Staden, R. RT A standard file format for data from DNA sequencing instruments. RL DNA Sequence 3, 107-110 (1992). RA Staden R.; RT "Software for sequence analysis."; RL Genome News 13:21-23(1993). RA Bonfield J.K., Smith K.F., Staden R.; RT "A New DNA Sequence Assembly Program."; RL Nucleic Acids Res. 23:4992-4999(1995). RA Bonfield, J.K. and Staden, R. RT The application of numerical estimates of base calling accuracy RT to DNA sequencing projects. RL Nucleic Acids Res. 23, 1406-1410 (1995). RA Bonfield, J.K. and Staden, R. RT Experiment files and their application during large-scale RT sequencing projects. RL DNA Sequence 6, 109-117 (1996). ADDRESS Medical Research Council, Cambridge, UK. CONTACT Rodger Staden RS@mrc-lmb.cam.ac.uk SITE WWW Server at URL http://www.mrc-lmb.cam.ac.uk/pubseq/ SITE-CONTACT Rodger Staden RS@mrc-lmb.cam.ac.uk OS Sun SPARC10 (solaris 2.5) eg SPARCstation 10/30 OS DEC ALPHA (Digital Unix 3.0/4.0) eg DEC 3000/500 OS SGI RIX) eg Indigo R4000 OS Linux 2.0 (Intel systems only) LANGUAGE FORTRAN, C, Xwindow, Tcl VOLUME - AC BC00259 NAME STATUS DOMAIN Sequence analysis DESCRIPTION Tools for managing large DNA-sequencing DESCRIPTION projects AUTHOR Dubnick M. RA Dubnick M.; RT "STATUS, SEQSTAT, CSTATUS and LOAD: computer programs that RT facilitate large DNA-sequencing projects."; RL Comput. Appl. Biosci. 8:291-292(1992). RX Medline; 92339044. RX SeqAnalRef; DUBM9201. ADDRESS Receptor Biochemistry and Molecular Biology Section ADDRESS NINDS/NIH, Bethesda, MD 20892, USA. CONTACT - SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/unix UNIX software are stored SITE as archive (tar) files compressed (.Z). SITE-CONTACT nethelp@ebi.ac.uk OS Unix LANGUAGE C VOLUME - AC BC00260 NAME XGRAIL DOMAIN Sequence analysis DESCRIPTION XGRAIL is a client-server implementation of a group of analysis DESCRIPTION tools for sequence exploration and gene discovery. DESCRIPTION This package allows the user to find protein coding regions in DESCRIPTION anonymous DNA sequences, to assemble gene models, translate part DESCRIPTION or all of these models, and search these translations against DESCRIPTION various databases. It also provides information about GC DESCRIPTION content, functional site identification (splice junctions, DESCRIPTION poly A sites, etc.) and the location of a variety of repetitive DESCRIPTION DNA sequences. AUTHOR - RA Uberbacher E.C., Mural R.J.; RT "Locating protein-coding regions in human DNA sequences RT by a multiple sensor-neural network approach."; RL Proc. Natl. Acad. Sci. USA 88(24):11261-11265(1991). RX Medline; 92107929. RX SeqAnalRef; UBEE9201. RA Mural R.J., Einstein J.R., Guan X., Mann R.C., Uberbacher E.C.; RT "An artificial intelligence approach to DNA sequence feature RT recognition."; RL Trends Biotechnol. 10:66-69(1992). RX Medline; 92181649. RX SeqAnalRef; MURR9201. RA Guan X., Mural R.J., Einstein J.R., Mann R.C., Uberbacher E.C.; RT "GRAIL: An Integrated Artificial Intelligence System for RT Gene Recognition and Interpretation."; RL Proc. The Eighth IEEE Conference on AI Applications, 9-13(1992). RA Uberbacher E.C., Einstein J.R., Guan X., Mural R.J.; RT "Gene Recognition and Assembly in the GRAIL system: RT Progress and Challenges."; RL Proc. The Sd International Conference on Bioinformatics, RL Supercomputing,and Complex Genome Analysis, eds. Lim, H. RL A., Fickett, J. W., Cantor, C. R. and Robbins, R. J. (World RL Sci., USA), pp. 465-476 (June 1992). RA XU Y., Mural R.J., Shah M.B., Uberbacher E.C.; RT "Recognizing Exons in Genomic Sequence Using GRAIL II."; RL (In) Genetic Engineering: Principles and Methods, Setlow J., Ed., RL 16:241-253, Plenum Press, New York, (1994). RX SeqAnalRef; XUYY9402. RA XU Y., Einstein J.R., Mural R.J., Shah M.B., Uberbacher E.C.; RT "An Improved System for Exon Recognition and Gene Modeling RT in Human DNA Sequences."; RL Proceedings of The 2nd International Conference on Intelligent RL Systems for Molecular Biology, AAAI Press (August 1994). RA XU Y., Mural R.J., Uberbacher E.C.; RT "Constructing Gene Models from Accurately-predicted Exons: RT An Application of Dynamic Programming." ; RL Comput. Appl. Biosci. 10:613-623(1994). RX SeqAnalRef; XUYY9403. RA Matis A., Mural R.J., Shah M.B., Uberbacher E.C.; RT "An Artificial Intelligence Method for Locating RT Promoters in Human DNA Sequences," RL To be submitted to Nucleic Acids Res. ADDRESS Informatics Group, Oak Ridge National Laboratory ADDRESS Oak Ridge, Tennessee, USA. CONTACT grail@ornl.gov (mailserver) CONTACT grailmail@ornl.gov (human) SITE ftp anonymous arthur.epm.ornl.gov SITE Directory /pub/xgrail/sun or /pub/xgrail/dec SITE-CONTACT - OS Sparc stations running Open Windows 3.0 and Sun OS 4.1.3, or OS on Dec Alpha workstations running the OSF/1 operating system. LANGUAGE - VOLUME - REQUIRES Connection of the user's machine to the Internet is required. AC BC00381 NAME PairWise and SearchWise DOMAIN Sequence analysis DOMAIN Protein sequence analysis DOMAIN Alignment Search software DOMAIN Searching databases DESCRIPTION PairWise and SearchWise allow the comparison of a protein DESCRIPTION sequence or protein profile to a DNA sequence, allowing DESCRIPTION for frame shifts and introns within the DNA sequence. DESCRIPTION This allows for confident use of corrupted and genomic DESCRIPTION DNA data in bioinformatics projects. DESCRIPTION PairWise is the one-on-one alignment program DESCRIPTION SearchWise is the database searching program DESCRIPTION Opensearch is a mneu driven program to submit searchwise DESCRIPTION jobs AUTHOR Ewan Birney RT - ADDRESS Sanger Centre, Wellcome Trust Genome Campus ADDRESS Hinxton, Cambridge CB10 1RQ, UK CONTACT birney@sanger.ac.uk SITE ftp anonymous ftp.sanger.ac.uk SITE Directory /pub/birney/wise SITE-CONTACT root@sanger.ac.uk SITE WWW Server at URL http://www.sanger.ac.uk/~birney/wise/topwise.html OS VMS, IRIX, solaris, OSF/1 LANGUAGE C VOLUME - REQUIRES - COMMENTS SearchWise is CPU intensive AC BC00391 NAME BCM Search Launcher DOMAIN WWW server DOMAIN Sequence format conversion tools DOMAIN Sequence analysis DOMAIN Protein sequence analysis DOMAIN Protein structure analysis DOMAIN Structure prediction DOMAIN Pattern Identification DOMAIN Alignment Search software DOMAIN Alignment editing and display DOMAIN Alignment browser DOMAIN Restriction maps DOMAIN Database and analysis DOMAIN Searching databases DOMAIN Statistical significance DOMAIN Comparative analysis SERVER http://www.hgsc.bcm.tmc.edu/SearchLauncher/ DESCRIPTION The BCM Search Launcher is an integrated set of World- DESCRIPTION Wide Web (WWW) pages that organize molecular biology- DESCRIPTION related search and analysis services available on the DESCRIPTION WWW by function, and provide a single point-of-entry for DESCRIPTION related searches. The Protein Sequence Search Page, for DESCRIPTION example, provides a single sequence entry form for DESCRIPTION submitting sequences to WWW servers that provide remote DESCRIPTION access to a variety of different protein sequence search DESCRIPTION tools, including BLAST, FASTA, Smith-Waterman, BEAUTY, DESCRIPTION PROSITE, and BLOCKS searches. Other Launch pages provide DESCRIPTION access to 1) nucleic acid sequence searches, 2) multiple DESCRIPTION and pairwise sequence alignments, 3) gene feature searches, DESCRIPTION 4) protein secondary structure prediction, and 5) DESCRIPTION miscellaneous sequence utilities (e.g., 6-frame DESCRIPTION translation). The BCM Search Launcher also provides a DESCRIPTION mechanism to extend the utility of other WWW services by DESCRIPTION adding supplementary hypertext links to results returned DESCRIPTION by remote servers. For example, links to the NCBI's DESCRIPTION Entrez database and to the Sequence Retrieval System DESCRIPTION (SRS) are added to search results returned by the NCBI's DESCRIPTION WWW BLAST server. These links provide easy access to DESCRIPTION auxiliary information, such as Medline abstracts, that DESCRIPTION can be extremely helpful when analyzing BLAST database DESCRIPTION hits. For new or infrequent users of sequence database DESCRIPTION search tools, we have pre-set the default search parameters DESCRIPTION to provide the most informative first-pass sequence DESCRIPTION analysis possible. We have also developed a batch client DESCRIPTION interface for Unix and Macintosh computers that allows DESCRIPTION multiple input sequences to be automatically searched as DESCRIPTION a background task, with the results returned as individual DESCRIPTION HTML documents directly to the user's system. AUTHOR Randall F. Smith, Brent A. Wiese, Mary K. Wojzynski, AUTHOR Daniel B. Davison , and Kim C. Worley RA Smith R.F., Wiese B.A., Wojzynski M.K., Davison D.B., Worley K.C.; RT "BCM Search Launcher--An integrated interface to molecular RT biology database search and analysis services available on RT the World-Wide Web."; RL Submitted. ADDRESS Randall F. Smith, Ph.D. ADDRESS Department of Molecular and Human Genetics, T-921, ADDRESS Baylor College of Medicine ADDRESS One Baylor Plaza, Houston, TX 77030, USA ADDRESS Tel: +1 (713) 798-4735 Fax: +1 (713) 798-5386 CONTACT rsmith@bcm.tmc.edu CONTACT kworley@bcm.tmc.edu SITE WWW Server at URL http://www.hgsc.bcm.tmc.edu/SearchLauncher/ SITE-CONTACT rsmith@bcm.tmc.edu SITE WWW Server at URL http://dot.imgen.bcm.tmc.edu:9331/downloads/software/batch_client.html SITE give information about the downloads SITE ftp anonymous dot.imgen.bcm.tmc.edu for a batch client SITE Directory /pub/software/search-launcher OS Unix and Macintosh for the batch client LANGUAGE Perl (on Unix), AppleScript (on Macintosh) VOLUME - REQUIRES MacTCP on Macintosh and AppleScript, Perl on Unix AC BC00423 NAME Pol3scan DOMAIN WWW server DOMAIN Sequence analysis SERVER http://irisbioc.bio.unipr.it/genomics.html DESCRIPTION Recognition of the eukaryotic internal control regions DESCRIPTION A box and B box that are typical of tRNA genes and DESCRIPTION tDNA-derived elements. The algorithm is based on the DESCRIPTION statistical analysis of a database of 231 tRNA DESCRIPTION promoter regions and makes use of weight matrices and DESCRIPTION weight vectors for scoring. The program discriminates DESCRIPTION between tRNA genes and related class III elements DESCRIPTION (e.g. tDNA-derived SINEs) on the basis of the presence DESCRIPTION of a transcriptional terminator signal and of the DESCRIPTION base-pairing within the aminoacyl stem. The accuracy DESCRIPTION of the prediction was estimated by scanning the DESCRIPTION eukaryotic nuclear sequences present in the rel. 33 of DESCRIPTION the EMBL database (65180 entries). The program DESCRIPTION correctly identified 932 of 940 known tRNA genes DESCRIPTION (0.85% of false negatives) with a false positive rate DESCRIPTION of 0.0018%. AUTHOR Pavesi A., Percudani R., Ottonello S.; RA Pavesi A., Conterio F., Bolchi A., Dieci G., and Ottonello S.; RT "Identification of new eucariotic tRNA genes in genomic databases RT by a multi weight matrix analysis of transcriptional control RT regions."; RL Nucleic Acids Res. 22:1247-1256 (1994). RX Medline; 94218250. RX SeqAnalRef; PAVA9401. ADDRESS Institute of Biochemical Sciences ADDRESS University of Parma ADDRESS Viale delle Scienze ADDRESS 43100 Parma, Italy CONTACT riccardo@irisbioc.bio.unipr.it SITE WWW Server at URL http://irisbioc.bio.unipr.it/pol3scan.html OS DOS,Unix LANGUAGE C VOLUME - REQUIRES - AC BC00426 NAME SAMSON DOMAIN Sequence analysis DOMAIN RNA analysis DOMAIN Protein structure analysis DESCRIPTION The SAMSON package is a tool for advanced analysis of DESCRIPTION primary DNA, RNA and protein structures. The package consists DESCRIPTION of 16 programs performing statistical analysis and comparison DESCRIPTION of biopolymer sequences, search for homologies, translation of DESCRIPTION DNA and RNA sequences into amino acid sequences, splicing of DESCRIPTION RNA sequences and restriction map construction, recognition of DESCRIPTION functionally related sites in biopolymer molecules, textual DESCRIPTION analysis of DNA and RNA regulatory sites and prediction of DESCRIPTION intermolecular hybridization sites in DNA and RNA molecules. DESCRIPTION The SAMSON package consists of: DESCRIPTION - 16 applied programs in form of executable modules under DESCRIPTION MS-DOS v. 3.0 or higher; DESCRIPTION - the Microsoft FORTRAN 5.0 source library containing DESCRIPTION standard input-output and simple sequence processing routines; DESCRIPTION - ASCII-files with manuals (in russian); DESCRIPTION - helpfiles and other things that are need for learning DESCRIPTION the software usage. AUTHOR Nazipova N.N., Shabalina S.A., Ogurtsov A.Yu., Kondrashov A.S., AUTHOR Roytberg M.A., Butryakov G.V., Vernoslov S.E.; RA Nazipova N.N., Shabalina S.A., Ogurtsov A.Yu., RA Kondrashov A.S., Roytberg M.A., Butryakov G.V., RA Vernoslov S.E.; RT "SAMSON: a software package for the biopolymer RT primary structure analysis."; RL Comput. Appl. Biosci. 11(4):423-426 (1995). ADDRESS Institute of Mathematical Problems of Biology, ADDRESS Russian Academy of Sciences, Pushchino, Moscow region,142292 Russia CONTACT NNN@impb.serpukhov.su or shab@imbp.serpukhov.su SITE - SITE-CONTACT - OS MS-DOS LANGUAGE MS FORTRAN 5.0 VOLUME - REQUIRES MS-DOS v. 3.0 or higher AC BC00428 NAME POLYAH, TSS, TSSG DOMAIN Sequence analysis DOMAIN e-mail Server ANALYSIS DOMAIN WWW server SERVER http://dot.imgen.bcm.tmc.edu:9331/gene-finder/gf.html SERVER service@bchs.uh.edu SERVER services@bioinformatics.weizmann.ac.il DESCRIPTION Analysis of uncharacterized human sequences DESCRIPTION TSSG and TSSW Recognition of human PolII promoter region DESCRIPTION and start of transcription. AUTHOR - RT - ADDRESS The Baylor College Of Medicine Computational Biology Group ADDRESS Houston, TX CONTACT solovyev@cmb.bcm.tmc.edu SITE WWW Server at URL http://dot.imgen.bcm.tmc.edu:9331/gene-finder/gf.html OS - LANGUAGE - VOLUME - REQUIRES - AC BC00435 NAME BEAUTY DOMAIN Sequence analysis DOMAIN Sequence tools DOMAIN Protein sequence analysis DOMAIN Database and analysis DOMAIN Searching databases DOMAIN Statistical significance DOMAIN Comparative analysis DOMAIN WWW server DESCRIPTION BEAUTY (BLAST Enhanced Alignment Utility) is an enhanced DESCRIPTION version of the NCBI's BLAST database search tool that DESCRIPTION facilitates identification of the functions of matched DESCRIPTION sequences. We have created new databases of conserved DESCRIPTION regions and functional domains for protein sequences in DESCRIPTION the NCBI's Entrez database, and BEAUTY allows this DESCRIPTION information to be directly incorporated into BLAST search DESCRIPTION results. A Conserved Regions Database, containing the DESCRIPTION locations of conserved regions within Entrez protein DESCRIPTION sequences, was constructed by 1) clustering the entire DESCRIPTION database into families, 2) aligning each family using our DESCRIPTION PIMA multiple sequence alignment program, and then DESCRIPTION 3) scanning the multiple alignments to locate the DESCRIPTION conserved regions within each aligned sequence. A DESCRIPTION separate Annotated Domains Database was constructed by DESCRIPTION extracting the locations of all annotated domains and DESCRIPTION sites from sequences represented in the Entrez, PROSITE, DESCRIPTION BLOCKS, and PRINTS databases. BEAUTY performs a BLAST DESCRIPTION search of those Entrez sequences with conserved regions DESCRIPTION and/or annotated domains. BEAUTY then uses the DESCRIPTION information from the Conserved Regions and Annotated DESCRIPTION Domains databases to generate, for each matched sequence, DESCRIPTION a schematic display that allows one to directly compare DESCRIPTION the relative locations of 1) the conserved regions, DESCRIPTION 2) annotated domains and sites, and 3) the locally-aligned DESCRIPTION regions matched in the BLAST search. In addition, BEAUTY DESCRIPTION search results include World-Wide Web hypertext links to DESCRIPTION a number of external databases that provide a variety of DESCRIPTION additional types of information on the function of matched DESCRIPTION sequences. This convenient integration of protein DESCRIPTION families, conserved regions, annotated domains, alignment DESCRIPTION displays, and World-Wide Web resources greatly enhances DESCRIPTION the biological informativeness of sequence similarity DESCRIPTION searches. Beauty searches can be performed remotely on DESCRIPTION our system using the "BCM Search Launcher" World-Wide-Web pages AUTHOR Kim C. Worley, Brent A. Wiese, and Randall F. Smith RA Worley K.C., Wiese B.A., Smith R.F.; RT "BEAUTY: An enhanced BLAST-based search tool that RT integrates multiple biological information resources RT into sequence similarity search results."; RL Genome Research 5:173-184 (1995). ADDRESS Kim C. Worley, Ph.D. ADDRESS Department of Molecular and Human Genetics ADDRESS T-929, Baylor College of Medicine ADDRESS One Baylor Plaza, Houston, TX 77030, USA ADDRESS Phone: +1 (713) 798-8292 FAX: +1 (713) 798-5386 CONTACT kworley@bcm.tmc.edu CONTACT brent@bcm.tmc.edu CONTACT rsmith@bcm.tmc.edu SITE WWW server at URL http://gc.bcm.tmc.edu:8088/search-launcher/launcher.html SITE-CONTACT rsmith@bcm.tmc.edu SITE ftp anonymous gc.bcm.tmc.edu for a batch client SITE Directory /pub/software/search-launcher OS Unix and Macintosh for the batch client LANGUAGE Perl (on Unix), AppleScript (on Macintosh) VOLUME - REQUIRES MacTCP on Macintosh and AppleScript, Perl on Unix AC BC00438 NAME PROMOTER SCAN DOMAIN Sequence analysis DESCRIPTION PROMOTER SCAN is designed to find putative eukaryotic Pol II promoter DESCRIPTION sequences in primary DNA sequence data. This program is experimental DESCRIPTION in nature, and should be used as an experimental tool. PROMOTER SCAN DESCRIPTION is best used to locate regions in primary DNA sequence that might be DESCRIPTION good candidate regions to further test for promoter functionality. At DESCRIPTION this time, based upon test promoter and non-promoter sequence sets, DESCRIPTION the program recognizes approximately 70% of all EPD primate promoter DESCRIPTION sequences, with a false positive rate of about one in every 17,200 DESCRIPTION bases. AUTHOR Dan S. Prestridge RA Prestridge, D.S.; RT "Predicting Pol II Promoter Sequences Using RT Transcription Factor Binding Sites."; RL J. Mol. Biol. 249(5):923-932 (1995). ADDRESS Advanced Biosciences Computing Center ADDRESS University of Minnesota ADDRESS 1479 Gortner Ave. ADDRESS St. Paul, MN 55108, USA ADDRESS Tel: +1 (612) 625-3744 - Fax : +1 (612) 625-5780 CONTACT danp@biosci.cbs.umn.edu SITE - SITE-CONTACT - OS UNIX(SUN, SGI, Dec Alpha,IBMRS6000) IBM PC LANGUAGE - VOLUME - REQUIRES - COMMENTS If you are interested in getting a copy of the program, send E-mail to COMMENTS danp@biosci.cbs.umn.edu for instructions. AC BC00452 NAME FSED DOMAIN WWW server DOMAIN Sequence analysis DOMAIN Sequence tools SERVER http://ir2lcb.cnrs-mrs.fr/d_fsed/fsed.html DESCRIPTION FSED has been developed to detect frameshift errors on new sequences. DESCRIPTION It is a more general approach than the one described before (Posfai and DESCRIPTION Roberts (1992). Proc. Natl. Acad. Sci. USA, 89: 4698-4702; Claverie DESCRIPTION (1993) J. Mol. Biol. 234: 1140-1157), as it does not rely on similarity DESCRIPTION searches. The method is based on the hypothesis that the coding DESCRIPTION constraints induce a statistical bias in the distribution of the DESCRIPTION 3-tuples and 6-tuples in the three frames of an open reading frame. DESCRIPTION This bias is used to derive discriminant functions on a learning set DESCRIPTION of sequences by applying a correspondence analysis. DESCRIPTION The method has been extensively tested on simulated frameshift errors DESCRIPTION and the results obtained have shown that its sensitivity and its DESCRIPTION selectivity rely upon the bias of the k-tuple distribution observed DESCRIPTION in the analyzed sequences. AUTHOR Fichant Gwennaele, Quentin Yves RA Fichant G., Quentin Y.; RT "A frameshift error detection algorithm for DNA sequencing projects."; RL Nucleic Acids Res. 23:2900-2908(1995). ADDRESS Dr. Gwennaele Fichant ADDRESS Institut de Genetique et Microbiologie ADDRESS Batiment 400 ADDRESS Centre Universitaire d'Orsay ADDRESS 91405 Orsay Cedex, France CONTACT gaf@igmors.u-psud.fr CONTACT quentin@lcb.cnrs-mrs.fr SITE WWW Server at URL http://ir2lcb.cnrs-mrs.fr/ SITE-CONTACT quentin@lcb.cnrs-mrs.fr OS - LANGUAGE - VOLUME - REQUIRES - AC BC00457 NAME MatInd and MatInspector DOMAIN Sequence analysis DOMAIN Database and analysis DESCRIPTION MatInd is a simple but powerful method to derive a DESCRIPTION matrix description of a consensus from a number of short sequences DESCRIPTION on which the definition of an IUPAC code would be based. DESCRIPTION MatInspector is a program that uses a large library of predefined DESCRIPTION matrix descriptions of transcription factor binding sites DESCRIPTION to locate matches in nucleotide sequences of unlimited length. DESCRIPTION It assigns a quality rating to matches and thus allows a quality- DESCRIPTION based filtering and selection of matches. AUTHOR Quandt, K., Frech, K., Karas, H., Wingender, E., Werner, T. RA Quandt, K., Frech, K., Karas, H., Wingender, E., Werner, T.: RT "MatInd and MatInspector - New fast and versatile tools for RT detection of consensus matches in nucleotide sequence data."; RL Nucleic Acids Res. 23:4878-4884(1995). ADDRESS - CONTACT quandt@gsf.de SITE ftp anonymous ariane.gsf.de SITE Directory /pub SITE-CONTACT quandt@gsf.de SITE WWW Server at URL http://www.gsf.de./biodv/matinspector.html OS UNIX,DOS,MacOS LANGUAGE C VOLUME - REQUIRES - AC BC00461 NAME DNA Stacks DOMAIN Sequence format conversion tools DOMAIN Sequence display DOMAIN Sequence editor DOMAIN Sequence analysis DOMAIN Sequence tools DOMAIN Protein sequence analysis DOMAIN Pattern Identification DOMAIN Alignment editing and display DOMAIN Alignment browser DOMAIN Genome Mapping Databases DOMAIN Phylogeny DESCRIPTION DNA Stacks (v. 1.1) is a HyperCard 2.x stack package DESCRIPTION for Macintosh computers featuring utilities for editing or DESCRIPTION coloring multiple DNA or protein sequence alignments, DESCRIPTION performing numerous data conversions or analyses related to DESCRIPTION molecular systematics, displaying auto-rescalable gene maps DESCRIPTION of mitochondrial or chloroplast genomes, extracting DNA DESCRIPTION gene sequences or translated protein sequences from about DESCRIPTION 26 animal mitochondrial genomes, and graphically depicting DESCRIPTION codon usage patterns. AUTHOR Eernisse, Douglas J. RA Eernisse, D. J.; RT "DNA Translator and Aligner: HyperCard utilities to aid RT phylogenetic analysis of molecules."; RL Comput. Appl. Biosci. 8:177-184(1992). RX Medline; 92274217. RX SeqAnalRef; EERD9201. ADDRESS D. J. Eernisse ADDRESS Dept. Biol. Sci. MH282 ADDRESS California State University ADDRESS Fullerton, CA 92634, USA CONTACT deernisse@fullerton.edu SITE ftp anonymous ftp.bio.indiana.edu SITE Directory /molbio/mac/ SITE-CONTACT archive@bio.indiana.edu SITE gopher Host: gopher://ftp.bio.indiana.edu Port: 70 SITE URL gopher://gopher://ftp.bio.indiana.edu:/70/11/IUBio-Software+Data/molbio/mac SITE WWW Server at URL http://biology.fullerton.edu/people/faculty/doug-eernisse/ OS MacOS LANGUAGE HyperTalk, C VOLUME 2 MB REQUIRES HyperCard 2.0 or greater, Macintosh AC BC00463 NAME SeqPup DOMAIN Sequence editor DOMAIN Sequence analysis DESCRIPTION SeqPup is a biological sequence editor and analysis program DESCRIPTION usable on the common computer systems including Macintosh, DESCRIPTION MS-Windows and X-Windows. It includes links to network DESCRIPTION services and external analysis programs. DESCRIPTION Features include DESCRIPTION multiple sequence alignment editor DESCRIPTION single sequence editor DESCRIPTION read and write several sequence file formats DESCRIPTION easy hand alignment features including colored bases and sliding DESCRIPTION automatic multiple sequence alignment with ClustalW app DESCRIPTION automatic gel fragment alignment to contigs with CAP app DESCRIPTION phylogenetic analysis of alignments with fastDNAml and LSADT apps DESCRIPTION phylogenetic tree drawing with DrawTree and DrawGram Phylip apps DESCRIPTION consensus, reverse, complement, degap, and distance/similarity operations DESCRIPTION restriction maps DESCRIPTION pretty print of alignments and sequences with boxed and shaded DESCRIPTION regions. DESCRIPTION translate dna to/from protein using various codon tables DESCRIPTION find strings and ORFs DESCRIPTION automatic preference saving DESCRIPTION internet send mail and sequence analysis services by email DESCRIPTION user-definable links to external analysis programs AUTHOR d. gilbert RT - ADDRESS biocomputing--indiana u--bloomington, in usa 47405 CONTACT SeqPup@Bio.Indiana.Edu SITE ftp anonymous iubio.bio.indiana.edu SITE Directory /molbio/seqpup SITE-CONTACT gilbertd@bio.indiana.edu SITE ftp anonymous iubio.bio.indiana.edu SITE Directory /util/dclap/source/ for the source code SITE-CONTACT gilbertd@bio.indiana.edu SITE WWW Server at URL http://iubio.bio.indiana.edu/IUBio-Software+Data/molbio/seqpup/ OS Macintosh, MS Windows, Unix/XWindow LANGUAGE C++ and C VOLUME - REQUIRES - AC BC00469 NAME OSA DOMAIN Sequence analysis DOMAIN Protein sequence analysis DOMAIN Epidemiology DOMAIN Phylogeny DOMAIN Statistical significance DOMAIN Comparative analysis DESCRIPTION OSA is a program to find, within an alignment of DESCRIPTION large sequences, those regions with an informative content DESCRIPTION similar to the displayed by the whole alignment and select, DESCRIPTION among them, the shortest empiricaly significant ones. The use of DESCRIPTION these short regions, instead of the larger ones, can save a DESCRIPTION considerable amount of time and resources in molecular screening DESCRIPTION or molecular epidemiology studies. AUTHOR Maria Jesus Martin, Joaquin Dopazo RA Martin M.J., Gonzalez-Candelas F., Sobrino F., Dopazo J.; RT "A method for determining the position and size of optimal RT sequence regions for phylogenetic analysis."; RL J. Mol. Evol. 41:1128-1138(1995). ADDRESS R&D Department, TDI ADDRESS c/ Condes de Torreanaz, 5 ADDRESS 28028, Madrid ADDRESS SPAIN CONTACT martin@tdi.es CONTACT dopazo@tdi.es SITE ftp anonymous ftp.tdi.es SITE Directory /pub/programas/ SITE-CONTACT martin@tdi.es SITE WWW Server at URL http://www.tdi.es/programas/osa-i.htm OS UNIX (Solaris, Irix) LANGUAGE GPC Pascal VOLUME 300K REQUIRES GPC for compiling sources COMMENTS OSA is available as both : executable file for Solaris or COMMENTS Irix operating systems and sources files. GPC compiler is COMMENTS only necessary if you download the sources. AC BC00470 NAME Primer Premier 4 DOMAIN Oligomer design and synthesis DOMAIN Sequence format conversion tools DOMAIN Sequence display DOMAIN Sequence editor DOMAIN Sequence analysis DOMAIN Sequence tools DOMAIN RNA analysis DOMAIN Restriction maps DESCRIPTION Primer Design Software DESCRIPTION Primer Premier 4 is now available for Power Macintosh and DESCRIPTION Window 3.1, NT as well as Windows 95. Primers can be DESCRIPTION designed for PCR, sequencing or hybridization probes DESCRIPTION automatically or with full manual control. DESCRIPTION From the selected pool of primers mutually compatible DESCRIPTION Nested/Multiplex primers or pairs can be chosen. DESCRIPTION Any primer can be mutated using the editing facility. DESCRIPTION Full degeneracy is supported. Comprehensive analyis of DESCRIPTION secondary structures as well as a table of properties DESCRIPTION including melting temperature calculated using nearest DESCRIPTION neighbor theory and optimal annealing temperature is DESCRIPTION displayed for each primer. DESCRIPTION DESCRIPTION The selected primers can be managed with the database DESCRIPTION storage facility. The program even makes the primer DESCRIPTION synthesis process painless by automatically creating an DESCRIPTION order form addressed to the vendor of your choice. DESCRIPTION DESCRIPTION Restriction enzyme analysis is available with multiple DESCRIPTION output formats: table, annotated sequence or map. Functions DESCRIPTION to edit the sequence and to translate it using standard or DESCRIPTION any mitochondrial/organelle codon table is provided. Graphs DESCRIPTION of melting temperature, internal stability and free energy DESCRIPTION are available on-line as well as in printed format. AUTHOR Premier Biosoft International RT - ADDRESS 3786 Corina Way ADDRESS Palo Alto, CA 94303 CONTACT sales@PremierBiosoft.com SITE WWW Server at URL http://www.PremierBiosoft.com OS Windows 95, 98, NT, 3.1, Power Macintosh LANGUAGE - VOLUME - REQUIRES - COMMENTS Commercial product, fully functional demo available at COMMENTS http://www.PremierBiosoft.com page. AC BC00471 NAME C library tools DOMAIN Sequence analysis DOMAIN Sequence tools DESCRIPTION We offer C libraries for those who develop DNA analysis DESCRIPTION tools for PC under MS DOS. Mini-database (so called data DESCRIPTION handler) is designed in object-oriented manner. It can hold DESCRIPTION different molecular-biological data in mode very DESCRIPTION appropriate for C/C++ programmer. There is also common DESCRIPTION virualization tool for the data stored in the data handler DESCRIPTION format files. AUTHOR A.A.Ptitsyn, D.A.Grigorovich RA Ptitsyn A.A., Grigorovich D.A.; RT "Object-oriented Data Handler for Sequence Analysis RT Software Development."; RL Comp. Appl. Biosci. 6:583-589(1995). ADDRESS 10, Lavrentiev ave. ADDRESS Institute of Cytology and Genetics ADDRESS Novosibirsk, RUSSIA. CONTACT ptitsyn@mailhost.bionet.nsc.ru CONTACT odip@mailhost.bionet.nsc.ru SITE ftp anonymous ftp.bionet.nsc.ru SITE Directory /pub/misc/userlibs.zip SITE-CONTACT odip@mailhost.bionet.nsc.ru SITE WWW Server at URL http://www.bionet.nsc.ru/ OS MS DOS LANGUAGE C/C++ VOLUME - REQUIRES IBM PC Compatible, 500K free base RAM 5M free HDD COMMENTS The documentation is still not translated in English COMMENTS at feb.1996 (Sorry). Probably you find useful other COMMENTS small routine libraries we put on FTP in the same ZIP. AC BC00472 NAME WWW-Query DOMAIN WWW server DOMAIN Sequence analysis DOMAIN Searching databases DOMAIN Multivariate analysis SERVER http://acnuc.univ-lyon1.fr/ DESCRIPTION WWW-Query is a World Wide Web server for browsing sequence DESCRIPTION collections structured under the ACNUC format and for performing DESCRIPTION multivariate analyses on sequences. General collections DESCRIPTION (GenBank, EMBL and NBRF) as well as specialized data banks DESCRIPTION (NRSub, Hovergen, HIDB and MGDB) can be accessed. The DESCRIPTION system allows complex queries to be constructed and the DESCRIPTION result of each query, represented by a list of sequences, is DESCRIPTION stored on the server. It is then possible to reuse this list DESCRIPTION to compute analyses on sequences. AUTHOR Perriere G., Thioulouse, J. RA Perriere, G. Thioulouse, J.; RT "On-line tools for sequence retrieval and multivariate RT statistics in molecular biology."; RL Comput. Applic. Biosci. 12:63-69(1996). ADDRESS Laboratoire de Biometrie, Genetique et Biologie des ADDRESS Populations - UMR CNRS 5558 ADDRESS Universite Claude Bernard - Lyon 1 ADDRESS 43, bd. du 11 Novembre 1918 ADDRESS 69622 Villeurbanne Cedex ADDRESS France CONTACT perriere@biomserv.univ-lyon1.fr SITE WWW Server at URL http://acnuc.univ-lyon1.fr/ OS UNIX LANGUAGE C, Fortran VOLUME - REQUIRES - AC BC00473 NAME Primers! for the Mac DOMAIN Oligomer design and synthesis DOMAIN Sequence analysis DESCRIPTION Primers! for the Mac is a shareware Macintosh application DESCRIPTION for picking primers for PCR and other applications. It DESCRIPTION allows the user to interactively scroll through all possible DESCRIPTION primers and primer pairs, to pick the optimal primer for DESCRIPTION his or her needs. AUTHOR Richard Resnick RT - ADDRESS - CONTACT rjr@applepi.com SITE ftp anonymous wuarchive.wustl.edu SITE Directory /systems/mac/info-mac/sci/primers-10-installer.hqx SITE-CONTACT - SITE WWW Server at URL http://www.applepi.com/macprimerinfo.html OS Macintosh LANGUAGE English VOLUME Approximately 300 KB REQUIRES Color Macintosh, System 7 or better, English Dialect AC BC00474 NAME LALNVIEW DOMAIN Sequence analysis DOMAIN Protein sequence analysis DOMAIN Alignment editing and display DESCRIPTION LALNVIEW is a graphical program for visualizing local DESCRIPTION alignments between two sequences (protein or nucleic acids). DESCRIPTION Sequences are represented by coloured rectangles to give DESCRIPTION an overall picture of their similarities. LALNVIEW is also DESCRIPTION able to display sequence features (active site, domain, DESCRIPTION motif, propeptide, etc.) along with the alignment. When DESCRIPTION using LALNVIEW through our Web servers, sequence features DESCRIPTION are automatically extracted from database annotations DESCRIPTION (SWISS-PROT, GenBank, EMBL or HOVERGEN) and displayed with DESCRIPTION the alignment. LALNVIEW is a useful tool for analysing DESCRIPTION pairwise sequence alignments and for making the link DESCRIPTION between sequence homology and what is known about the DESCRIPTION structure or function of these sequences. AUTHOR Laurent Duret RT - ADDRESS Department of Medical Biochemistry, ADDRESS University of Geneva, ADDRESS 1 rue Michel Servet, ADDRESS CH-1211 Geneva 4, Switzerland CONTACT duret@dim.hcuge.ch SITE ftp anonymous expasy.hcuge.ch SITE Directory /pub/lalnview SITE-CONTACT duret@dim.hcuge.ch SITE WWW Server at URL http://expasy.hcuge.ch/sprot/lalnview.html OS UNIX, PC, Macintosh LANGUAGE ANSI C, SUIT VOLUME 1 Mb REQUIRES color screen AC BC00484 NAME SorFind DOMAIN Sequence analysis DESCRIPTION Identification of protein coding regions in genomic DNA Sequence DESCRIPTION SorFind is a DOS-based computer program that accepts a DESCRIPTION DNA sequence as input in one of several formats, and produces DESCRIPTION as output the same sequence in GenBank or EMBL format with DESCRIPTION a feature table added to annotate the location of putative coding DESCRIPTION exons. The program was first published in 1992 as a method to DESCRIPTION search for first exons only, but has since been revised and DESCRIPTION improved. AUTHOR Gordon B. Hutchinson RA Hutchinson, G.B., and Hayden, M.R.; RT "The prediction of exons through an analysis of spliceable RT open reading frames."; RL Nucleic Acids Res. 20:(13)3453-3462(1992). RX Medline; 92334998. RX SeqAnalRef; HUTG9201. ADDRESS c/o RabbitHutch Biotechnology ADDRESS P.O. Box 506 ADDRESS 108 Mile Ranch, B.C. ADDRESS Canada V0K 2Z0 CONTACT hutch@netshop.bc.ca SITE ftp anonymous iubio.bio.indiana.edu SITE Directory /molbio/ibmpc SITE-CONTACT - OS MS-DOS LANGUAGE C++ VOLUME - REQUIRES 386 or better microprocessor COMMENTS The software works in tandem with two other programs, COMMENTS RepFind (identifies common repetitive elements) and PromFind COMMENTS (identifies promoter regions) A full GUI under Windows95 is COMMENTS under commercial development, integrating the three COMMENTS programs. AC BC00485 NAME PromFind DOMAIN Sequence analysis DESCRIPTION PromFind is a DOS-based computer program that accepts a DESCRIPTION DNA sequence as input in one of several formats, and produces DESCRIPTION as output the same sequence in GenBank or EMBL format with DESCRIPTION a feature table added to annotate the location of putative DESCRIPTION promoter regions. The program does not advise whether or not DESCRIPTION a promoter is present, but rather assumes one is present and DESCRIPTION makes one prediction as to its location per sequence segment DESCRIPTION (specified by the user). AUTHOR Gordon B. Hutchinson RA Hutchinson, Gordon. B.; RT "The Prediction of Vertebrate Promoter Regions Using RT Differential Hexamer Frequency Analysis."; RL Comput. Appl. Biosci. (in press) ADDRESS c/o RabbitHutch Biotechnology ADDRESS P.O. Box 506 ADDRESS 108 Mile Ranch, B.C. ADDRESS Canada V0K 2Z0 CONTACT hutch@netshop.bc.ca SITE ftp anonymous iubio.bio.indiana.edu SITE Directory /molbio/ibmpc SITE-CONTACT - OS MS-DOS LANGUAGE C++ VOLUME - REQUIRES 386 or better microprocessor COMMENTS The software works in tandem with two other programs, COMMENTS RepFind (identifies common repetitive elements) andSorFind COMMENTS (identifies coding regions) A full GUI under Windows95 is COMMENTS under commercial development, integrating the three COMMENTS programs. AC BC00486 NAME RepFind DOMAIN Sequence analysis DESCRIPTION Identification of promoter regions in vertebrate DNA sequence DESCRIPTION RepFind is a DOS-based computer program that accepts a DESCRIPTION DNA sequence as input in one of several formats, and produces DESCRIPTION as output the same sequence in GenBank format with a feature DESCRIPTION table added to annotate the location and identity of common DESCRIPTION repeat elements. As a default the program identifies known DESCRIPTION human repeat elements, but it can be user-extended to identify DESCRIPTION any sequence of interest to the researcher. Several options DESCRIPTION allow control of the output, including a feature that replaces all DESCRIPTION repeat nucleotides with the letter "n" to facilitate database DESCRIPTION searches. The program may also be modified to identify and DESCRIPTION exclude vector sequence. AUTHOR Gordon B. Hutchinson RT - ADDRESS c/o RabbitHutch Biotechnology ADDRESS P.O. Box 506 ADDRESS 108 Mile Ranch, B.C. ADDRESS Canada V0K 2Z0 CONTACT hutch@netshop.bc.ca SITE ftp anonymous iubio.bio.indiana.edu SITE Directory /molbio/ibmpc SITE-CONTACT - OS MS-DOS LANGUAGE C++ VOLUME - REQUIRES 386 or better microprocessor COMMENTS The software works in tandem with two other programs, COMMENTS PromFind (identifies promoter regions) andSorFind COMMENTS (identifies coding regions) A full GUI under Windows95 is COMMENTS under commercial development, integrating the three COMMENTS programs. AC BC00490 NAME ConsInspector DOMAIN Sequence analysis DESCRIPTION ConsInspector uses a precompiled library of extended weight DESCRIPTION matrix descriptions (consensus profiles) of transcription DESCRIPTION factor binding sites to scan nucleic acid sequences for DESCRIPTION matches to these sites. AUTHOR K. Frech, G. Herrmann, T. Werner RA Frech, K., Herrmann, G., Werner, T.; RT "Computer-assisted prediction, classification, and delimitation RT of protein binding sites in nucleic acids."; RL Nucl. Acids Res. 21:1655 - 1664 (1993). RA Frech, K., Dietze, P., Werner, T.; RT "ConsInspector 3.0: new library and enhanced functionality."; RL Comput. App. Biosci. 13(1):109-110(1997). ADDRESS GSF - National Research Center for Environment and Health ADDRESS Institute of Mammalian Genetics ADDRESS D-85764 Neuherberg, Germany CONTACT frech@gsf.de SITE ftp anonymous ariane.gsf.de SITE Directory /pub SITE-CONTACT frech@gsf.de, quandt@gsf.de SITE WWW Server at URL http://www.gsf.de/biodv/consinspector.html OS UNIX,VAX/VMS,DOS,MacOS LANGUAGE C VOLUME - REQUIRES - AC BC00491 NAME CoreSearch DOMAIN Sequence analysis DESCRIPTION Identification of consensus elements in a set of unaligned DESCRIPTION nucleic acid sequences. AUTHOR F. Wolfertstetter, K. Frech, T. Werner RA Wolfertstetter, F., Frech, K., Herrmann, G., Werner, T.; RT "Identification of functional elements in unaligned nucleic RT acid sequences by a novel tuple search algorithm."; RL Comp. Applic. Biosci. 12:71-80 (1996). ADDRESS GSF - National Research Center for Environment and Health ADDRESS Institute of Mammalian Genetics ADDRESS D-85764 Neuherberg, Germany CONTACT frech@gsf.de SITE ftp anonymous ariane.gsf.de SITE Directory /pub/unix SITE-CONTACT frech@gsf.de, quandt@gsf.de SITE WWW Server at URL http://www.gsf.de/biodv/coresearch.html OS UNIX LANGUAGE C VOLUME - REQUIRES - AC BC00495 NAME BlueGene DOMAIN Neural Networks DOMAIN Searching databases DOMAIN Sequence display DOMAIN Sequence editor DOMAIN Sequence analysis DOMAIN Protein sequence analysis DOMAIN Structure prediction DOMAIN Database and analysis DESCRIPTION BlueGene uses a fast neural network for sequence similarity DESCRIPTION searches in Genbank and SWISS-PROT databases. DESCRIPTION BlueGene also includes graphically tools for sequence DESCRIPTION editing and analysing. DESCRIPTION BlueGene uses given and new sequence features to annotate DESCRIPTION the sequence editor and the map. AUTHOR Magic Works GmbH RT - ADDRESS Magic Works GmbH ADDRESS Potsdamer Str. 18a ADDRESS D-14513 Teltow ADDRESS GERMANY CONTACT info@magic-works.com SITE WWW Server at URL http://www.bluegene.com/ SITE-CONTACT - OS Win 3.1x or higher LANGUAGE - VOLUME 3.1MB REQUIRES 16MB RAM COMMENTS A free BlueGene demo version is ready for downloading on COMMENTS http://www.bluegene.com/. AC BC00497 NAME Sequin DOMAIN Sequence format conversion tools DOMAIN Sequence display DOMAIN Sequence editor DOMAIN Sequence analysis DOMAIN Sequence tools DOMAIN Alignment editing and display DOMAIN Alignment browser DOMAIN Sequence data submissions DESCRIPTION Sequin is a stand-alone software tool developed by the NCBI DESCRIPTION for submitting entries to the GenBank, EMBL, or DDBJ DESCRIPTION sequence databases. It is capable of handling simple DESCRIPTION submissions which contain a single short mRNA sequence, and DESCRIPTION complex submissions containing long sequences, multiple DESCRIPTION annotations, segmented sets of DNA, or phylogenetic and DESCRIPTION population studies. AUTHOR Jonathan Kans, Colombe Chappey RT - ADDRESS NIH/NLM/NCBI ADDRESS Building 38A, Room 8N805 ADDRESS Bethesda, MD 20894 ADDRESS U.S.A. CONTACT info@ncbi.nlm.nih.gov SITE ftp anonymous ncbi.nlm.nih.gov SITE Directory /sequin SITE-CONTACT info@ncbi.nlm.nih.gov SITE WWW Server at URL http://www.ncbi.nlm.nih.gov/Sequin OS Mac (68K and PPC), Windows (16 and 32 bit), Unix (Sun, Solaris, SGI, Linux, DEC) LANGUAGE English VOLUME - REQUIRES - COMMENTS Information about this package is available from COMMENTS http://www.ncbi.nlm.nih.gov/Sequin AC BC00500 NAME DnaSP DOMAIN Sequence format conversion tools DOMAIN Sequence analysis DOMAIN Sequence tools DOMAIN Population Genetics DESCRIPTION DnaSP is a software package for Windows that DESCRIPTION performs extensive population genetics analyses on DNA DESCRIPTION sequence data. DESCRIPTION DnaSP estimates several measures of DNA sequence DESCRIPTION polymorphism within and between populations (in noncoding, DESCRIPTION synonymous or nonsynonymous sites), linkage disequilibrium, DESCRIPTION recombination, gene flow, and gene conversion. DESCRIPTION The program can also perform the analysis of the pairwise DESCRIPTION differences distribution (mismatch distribution), and the DESCRIPTION frequency spectrum in constant size and in growing populations. DESCRIPTION DnaSP can also conduct some neutrality tests: Fu and DESCRIPTION Li's; Hudson, Kreitman and Aguade; McDonald and Kreitman; DESCRIPTION and Tajima's tests. DESCRIPTION DnaSP can estimate the confidence intervals of some test- DESCRIPTION statistics by the coalescent. DESCRIPTION DnaSP allows performing several analyses by the sliding window DESCRIPTION method, and also to obtain graphic representations. DESCRIPTION Input: Aligned DNA sequences in NBRF/PIR, MEGA, PHYLIP and NEXUS DESCRIPTION file formats. DESCRIPTION Output: the results are displayed in tables and graphs. The DESCRIPTION output can be either sent to the printer or saved in a file. DESCRIPTION The program can handle a large number of sequences (hundreds) DESCRIPTION of thousands of nucleotides each. AUTHOR Julio Rozas and Ricardo Rozas RT "DnaSP version 3: an integrated program for molecular population RT genetics and molecular evolution analysis" RL Bioinformatics 15: 174-175 (1999). ADDRESS Departament de Genetica ADDRESS Facultat de Biologia ADDRESS Universitat de Barcelona ADDRESS Diagonal 645 ADDRESS Barcelona 08071 ADDRESS Spain ADDRESS Phone: +34 93-4021495 ADDRESS Fax: +34 93-4110969 CONTACT julio@porthos.bio.ub.es SITE WWW Server at URL http://www.bio.ub.es/~julio/DnaSP.html SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/dos/dnasp SITE-CONTACT nethelp@ebi.ac.uk SITE DnaSP updates: SITE WWW Server at URL http://www.bio.ub.es/~julio/DnaSP.html OS Winodws 95, 98, NT LANGUAGE Visual Basic 5.0 VOLUME 3992 Kb REQUIRES PC Pentium, 16 Mb RAM COMMENTS For academic uses, DnaSP is available free of charge AC BC00507 NAME NJPLOT DOMAIN Protein sequence analysis DOMAIN Sequence analysis DOMAIN Phylogeny DESCRIPTION NJPLOT is a phylogenetic tree drawing program that handles DESCRIPTION files describing trees by the nested parentheses method DESCRIPTION (e.g. PHYLIP-built trees). DESCRIPTION Features: DESCRIPTION A graphical interface allows to re-root a tree anywhere and DESCRIPTION to swap branches. DESCRIPTION Bootstrap values are displayed next to internal branches. DESCRIPTION Branch lengths can be optionally displayed. DESCRIPTION Tree plots can be saved to a PostScript file (a PICT file DESCRIPTION on Macintosh) for printing. AUTHOR Manolo Gouy RT - ADDRESS Laboratoire de biometrie, genetique et biologie des populations ADDRESS UMR CNRS 5558 ADDRESS Universite C. Bernard - Lyon 1 ADDRESS 69622 Villeurbanne, France CONTACT mgouy@biomserv.univ-lyon1.fr SITE ftp anonymous biom3.univ-lyon1.fr SITE Directory /pub/mol_phylogeny/njplot SITE-CONTACT - OS DOS, Unix, Macintosh LANGUAGE - VOLUME - REQUIRES - AC BC00510 NAME CBLAST DOMAIN Sequence analysis DOMAIN Protein sequence analysis DOMAIN Searching databases DESCRIPTION CBLAST is a post-processor for BLAST that DESCRIPTION sorts the results of a BLAST sequence similarity search DESCRIPTION according to sequence membership in user-defined 'clusters' DESCRIPTION of sequences. We have demonstrated the utility of this DESCRIPTION application by constructing two cluster databases. The DESCRIPTION first describes clusters of nucleotide sequences DESCRIPTION representing the same gene, as documented in the UNIGENE DESCRIPTION database, and the second describes clusters of protein DESCRIPTION sequences which are members of the protein families DESCRIPTION documented in the PROSITE database. Cluster databases and DESCRIPTION the CBLAST post-processor provide an efficient mechanism DESCRIPTION for identifying and exploring relationships and DESCRIPTION dependencies between new sequences and database entries. AUTHOR Greg S. Miller, Rainer Fuchs RA Miller, G.S. and Fuchs R.; RT "Post-processing of BLAST results using databases RT of clustered sequences."; RL Comput. Appl. Biosci. 13:81-87(1997). ADDRESS Glaxo Wellcome Research and Development ADDRESS 5 Moore Drive ADDRESS Research Triangle Park, NC 27709 ADDRESS USA CONTACT gsm15414@glaxowellcome.com SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/unix SITE-CONTACT software@ebi.ac.uk OS UNIX LANGUAGE C, perl VOLUME - REQUIRES yacc, lex (or bison, flex) AC BC00511 NAME DIALIGN1.0 DOMAIN Sequence analysis DOMAIN Protein sequence analysis DESCRIPTION A novel algorithm for pairwise as well as multiple alignment DESCRIPTION of nucleic acid and protein sequences DESCRIPTION DIALIGN is an alignment program that relies on comparison of DESCRIPTION whole segments of the sequences instead of comparison of DESCRIPTION single residues. Multiple alignments are constructed by DESCRIPTION using local pairwise alignments. DESCRIPTION The program is especially suited to detect local DESCRIPTION similarities in otherwise completely unrelated sequences. DESCRIPTION DIALIGN does not use any gap penalty, thus avoiding this DESCRIPTION critical parameter. For protein sequences or short DNA DESCRIPTION sequences no parameter has to be set. There is only one DESCRIPTION parameter the user has to set if long DNA sequences DESCRIPTION (length > 400 bp) are to be aligned. AUTHOR Burkhard Morgenstern, Andreas Dress, Thomas Werner RA B. Morgenstern, A. Dress, T. Werner: RT "Multiple DNA and protein sequence alignment based on RT segment-to-segment comparison" RL Proc. Natl. Acad. Sci. 93:12098-12103(1996). ADDRESS Dr. Burkhard Morgenstern ADDRESS GSF - National Research Center for Environment and Health, ADDRESS Institute of Biomathematics and Biometry ADDRESS Ingolstaedter Landstr. 1, ADDRESS 85764 Neuherberg, ADDRESS Germany CONTACT morgenstern@gsf.de SITE WWW Server at URL http://www.gsf.de/biodv/dialign.html SITE-CONTACT - OS UNIX(DEC, SGI, CONVEX, HP, SUN) LANGUAGE - VOLUME - REQUIRES - AC BC00520 NAME Miropeats DOMAIN Sequence format conversion tools DOMAIN Sequence analysis DOMAIN Sequence tools DOMAIN Alignment Search software DOMAIN Alignment editing and display DESCRIPTION Miropeats is a graphical DNA sequence comparison tool. DESCRIPTION It can be used in almost all situations where one would DESCRIPTION normally use sequence alignments or dot plots to compare DESCRIPTION DNA sequences. However, Miropeats improves on dotplots DESCRIPTION in two ways, firstly, by allowing multiple sequences to DESCRIPTION be compared simultaneously and, secondly, by usually DESCRIPTION presenting a realtively intuitive graphic. It improves DESCRIPTION on large alignments by summarising all the similarities DESCRIPTION on a single page of PostScript (TM) graphics. AUTHOR Jeremy Parsons RA Parsons J.D.; RT "Miropeats: graphical DNA sequence comparisons."; RL Comput. Appl. Biosci. 11(6):615-619(1995). RA Parsons J.D.; RT "Improved tools for DNA comparison and clustering."; RL Comput. Appl. Biosci. 11(6):603-613(1995). ADDRESS European Bioinformatics Institute, ADDRESS Wellcome Trust Genome Campus, ADDRESS Hinxton, ADDRESS Cambridge ADDRESS CB10 1SD ADDRESS England CONTACT Jeremy.Parsons@ebi.ac.uk SITE WWW Server at URL http://genome.wustl.edu/est/esthmpg.html OS Solaris, IRIX, OSF, UNIX LANGUAGE C-shell, ANSI-C VOLUME - REQUIRES PostScript printing or viewing AC BC00522 NAME Primers! for the WWW DOMAIN Sequence analysis DOMAIN Genetic tools DOMAIN Oligomer design and synthesis DOMAIN WWW server SERVER http://www.williamstone.com/primers DESCRIPTION Free oligonucleotide design and analysis online. AUTHOR Richard Resnick, Williamstone Enterprises Inc. RA Resnick, R.; RT "Primers! for the WWW"; RL http://www.williamstone.com (1997). ADDRESS 46A Cedar St. ADDRESS Waltham, MA 02154 CONTACT rjr@williamstone.com SITE WWW Server at URL http://www.williamstone.com/primers OS All LANGUAGE Perl VOLUME n/a REQUIRES Any Graphical WWW Browser AC BC00523 NAME PromFD DOMAIN Sequence analysis DESCRIPTION PromFD is a computer program that predicts vertebrate DESCRIPTION RNA pol II promoters. In the development of PromFD, both DESCRIPTION vertebrate promoters, obtained from the Eukaryotic Promoter DESCRIPTION Database, and non promoter sequences, obtained fro the GenBank, DESCRIPTION were used. Both the promoters and non-promoters were divided DESCRIPTION into a training set and a test set. Sequence patterns that DESCRIPTION were found to occur much more frequently in the training set DESCRIPTION promoters were selected into the PromFD database. The program DESCRIPTION PromFD scores input DNA sequences according to the PromFD DESCRIPTION database. It predicts the locations of potential promoters DESCRIPTION and the locations of corresponding TATA boxes, if found. The DESCRIPTION program detects 71% training set promoters with a false DESCRIPTION positive rate of 1 in 13000 bp, 47% test set promoters with DESCRIPTION a false positive rate of 1 in 9800 bp. AUTHOR Qing K Chen, Gerald Z Hertz, Gary D Stormo RA Qing K Chen, Gerald Z Hertz, Gary D Stormo RT "PromFD 1.0: a computer program that predicts RT eukaryotic Pol II promoters using strings and RT IMD matrices."; RL Compt. Appl. Biosci. 13:29-35(1997). ADDRESS Dept. of Molecular, Cellular, and Developmental Biology ADDRESS University of Colorado, Boulder, CO 80309-0347 ADDRESS USA CONTACT chenq@ural.colorado.edu SITE - SITE-CONTACT - OS unix LANGUAGE C++ VOLUME - REQUIRES - AC BC00524 NAME RepeatMasker DOMAIN Sequence analysis DOMAIN Searching databases DOMAIN e-mail Server ANALYSIS DOMAIN WWW server SERVER repeatmasker@ftp.genome.washington.edu DESCRIPTION RepeatMasker screens DNA sequences in fasta format against DESCRIPTION a library of mammalian repetitive elements and returns DESCRIPTION a masked query sequence ready for database searches DESCRIPTION as well as a table annotating the masked regions in detail. AUTHOR Arian F.A. Smit, Phil Green RT - ADDRESS Department of Molecular Biotechnology Genome Center ADDRESS University of Washington, Box 352145 ADDRESS Seattle, WA 98195-2145 CONTACT asmit@u.washington.edu SITE WWW Server at URL http://ftp.genome.washington.edu/cgi-bin/RepeatMasker OS Unix LANGUAGE Perl, C VOLUME - REQUIRES - AC BC00527 NAME tRNAscan-SE DOMAIN Sequence analysis DOMAIN RNA analysis DOMAIN WWW server DOMAIN Statistical significance SERVER http://genome.wustl.edu/eddy/tRNAscan-SE/ DESCRIPTION tRNAscan-SE identifies transfer RNA genes in genomic DNA or DESCRIPTION RNA sequences. It combines the specificity of the Cove DESCRIPTION probabilistic RNA prediction package (Eddy & Durbin, 1994) DESCRIPTION with the speed and sensitivity of tRNAscan 1.3 (Fichant & DESCRIPTION Burks, 1991) plus an implementation of an algorithm described DESCRIPTION by Pavesi and colleagues (1994) which searches for DESCRIPTION eukaryotic pol III tRNA promoters. tRNAscan-SE identifies DESCRIPTION 99-100% of transfer RNA genes in DNA sequence while giving DESCRIPTION less than one false positive per 15 gigabases. The program DESCRIPTION searches at approximately 30,000 bp per second. Other DESCRIPTION features include prediction of tRNA secondary structure, DESCRIPTION and detection of unusual tRNA homologues such as DESCRIPTION selenocysteine tRNAs, tRNA-derived repetitive elements and DESCRIPTION tRNA pseudogenes. AUTHOR Todd M. Lowe, Sean R. Eddy RA Lowe T.M., Eddy S.R.; RT "tRNAscan-SE: a program for improved detection RT of transfer RNA genes in genomic sequence."; RL Nucleic Acids Res 25: 955-964 (1997). RA Eddy, S.R., Durbin, R.; RT "RNA Sequence Analysis Using Covariance Models"; RL Nucleic Acids Res. 22: 2079-2088 (1994). RA Fichant G.A., Burks C.; RT "Identifying potential tRNA genes in genomic RT DNA sequences"; RL J Mol Biol 220: 659-671 (1991). RA Pavesi A., Conterio F., Bolchi A., Dieci G., RA Ottonello S.; RT "Identification of new eukaryotic tRNA genes in RT genomic databases by a multistep weight matrix RT analysis of transcriptional control regions."; RL Nucleic Acids Res. 22:1247-1256 (1994). ADDRESS Dept. of Genetics ADDRESS Washington University School of Medicine ADDRESS 660 S. Euclid, Box 8232 ADDRESS St. Louis MO 63110 CONTACT lowe@genetics.wustl.edu SITE WWW Server at URL http://genome.wustl.edu/eddy/tRNAscan-SE/ OS UNIX LANGUAGE C, Perl VOLUME - REQUIRES Perl 5.0+ AC BC00528 NAME Bielefeld University Bioinformatics Server DOMAIN Sequence analysis DOMAIN Sequence tools DOMAIN Protein sequence analysis DOMAIN Alignment Search software DOMAIN Genetic tools DOMAIN Phylogeny DOMAIN WWW server SERVER http://bibiserv.TechFak.Uni-Bielefeld.DE/ DESCRIPTION BibiServ is both, a fast computer to run web-based DESCRIPTION bioinformatics software and an integration point for DESCRIPTION the bioinformatics activities at Bielefeld University. AUTHOR multiple authors RT - ADDRESS University of Bielefeld ADDRESS Technische Fakultaet, AG PI ADDRESS PB 100 131 ADDRESS D - 33501 Bielefeld ADDRESS Germany CONTACT bibi@TechFak.Uni-Bielefeld.DE SITE WWW Server at URL http://bibiserv.TechFak.Uni-Bielefeld.DE/ OS any LANGUAGE English VOLUME - REQUIRES Netscape Navigator > 3.0 AC BC00529 NAME The USC Sequence Alignment Package DOMAIN Sequence analysis DOMAIN Sequence tools DOMAIN Protein sequence analysis DOMAIN Pattern Identification DOMAIN Alignment Search software DOMAIN Statistical significance DOMAIN WWW server SERVER http://www-hto.usc.edu/software/seqaln/ DESCRIPTION This library of functions aligns nucleotide and DESCRIPTION protein sequences finding global, local, overlapping, DESCRIPTION and fitting regions of alignment using the generalized DESCRIPTION Smith-Waterman linear gap function g(k) = DESCRIPTION a + b(k-1) with one or two DNA, RNA or one-letter coded protein sequences. Also finds DESCRIPTION statistical significance of local alignments using the Poisson clumping heuristic. DESCRIPTION DESCRIPTION The package also includes GFSR, a good pseudorandom number generator, and standalone DESCRIPTION programs to perform global, local, fit and overlap alignments. AUTHOR Paul Hardy, Michael S. Waterman RT - ADDRESS Department of Mathematics ADDRESS University of Southern California ADDRESS 1042 W. 36th Place, DRB 155 ADDRESS Los Angeles, CA 90089-1113 CONTACT phardy@hto.usc.edu SITE WWW Server at URL http://www-hto.usc.edu/software/seqaln/ OS - LANGUAGE C VOLUME - REQUIRES - AC BC00532 NAME CODONTREE DOMAIN Sequence analysis DESCRIPTION The classic triplet code responsible for the translation DESCRIPTION of a mRNA sequence into the amino acid sequence of a DESCRIPTION protein was the first deciphered code of the genetic DESCRIPTION language. Owing to the degeneration of the genetic code, DESCRIPTION different triplets (codon families) can code for the DESCRIPTION same amino acid. As soon as the first nucleotide DESCRIPTION sequences were produced, it was immediately clear DESCRIPTION that for a given gene the usage of different synonymous DESCRIPTION codons was not random but rather species specific, DESCRIPTION and also linked to its expression and/or to the DESCRIPTION genetic compartment where it was located. DESCRIPTION The algorithm CODONTREE has been devised in order to DESCRIPTION investigate the linguistic properties of coding regions, DESCRIPTION that is, their codon strategy. DESCRIPTION CODONTREE is able to determine: DESCRIPTION codon usage table for a set of protein coding genes; DESCRIPTION gene relationship on the basis of codon usage similarity; DESCRIPTION compositional features of protein coding genes DESCRIPTION (e.g. bases composition at various codon positions). AUTHOR Graziano Pesole, Marcella Attimonelli, Sabino Liuni RA Pesole G., Attimonelli M., and Liuni S.; RT "A backtranslation method based on codon usage strategy"; RL Nucleic Acids Res. 16:1715-1728(1988). ADDRESS Sabino Liuni ADDRESS Area di Ricerca CNR ADDRESS Via Amendola 166/5 ADDRESS 70126 Bari (Italy) CONTACT sabino@area.ba.cnr.it SITE WWW Server at URL OS Unix, PC-DOS LANGUAGE C VOLUME - REQUIRES - AC BC00533 NAME DNAmend DOMAIN Sequence display DOMAIN Sequence editor DOMAIN Sequence analysis DOMAIN Sequence tools DOMAIN Genetic tools DOMAIN Restriction maps DESCRIPTION DNAmend is cloning software. That means, it may serve DESCRIPTION lab-workers in molecular biology and genetic engineering to DESCRIPTION monitor the DNA-cloning process. The PC routine provides DESCRIPTION on-line control on the steps of a cloning protocol - DESCRIPTION including the selection of the vectors and fragments, their DESCRIPTION processing by restrictase digestion, subsequent ligation, DESCRIPTION and the analysis of the cloned DNA. DESCRIPTION The software is designed to accept files containing DNA DESCRIPTION sequence information in any file format based on PC-text. DESCRIPTION A set of pull-down menu commands enables the user to change DESCRIPTION the mode of viewing the DNA-sequences, print them out, and DESCRIPTION above all manipulate them. One can search DNA sequences for DESCRIPTION restriction sites, open reading frames and certain sequence DESCRIPTION patterns, translate the sequences and simulate Restriction, DESCRIPTION Ligation or End modification on-line. DESCRIPTION One may export maps of the DNA-sequences via clipboard into DESCRIPTION other Windows applications to prepare them for publishing. DESCRIPTION The program contains a detailed on-line help. AUTHOR Piet Jonas & Bjoern Maul - ADDRESS Dr. Bjoern Maul ADDRESS B.-Lichtenberg-Str. 10 ADDRESS 10407 Berlin ADDRESS Germany CONTACT maul@fmp-berlin.de SITE WWW Server at URL http://pc13mi.biologie.uni-greifswald.de/sequenz.html OS Microsoft Windows LANGUAGE Turbo Pascal VOLUME 500 KB disc space REQUIRES IBM-PC, 4 MB RAM, Windows 3.x/95/NT COMMENTS Download a free Demo-Version at COMMENTS http://pc13mi.biologie.uni-greifswald.de/sequenz.html AC BC00541 NAME Plasmid Premier DOMAIN Sequence display DOMAIN Sequence editor DOMAIN Sequence analysis DOMAIN Restriction maps DESCRIPTION PLASMID PREMIER is a fully featured vector analysis and DESCRIPTION publication quality graphics tool. It provides vector DESCRIPTION analysis tools including restriction enzymes, motifs, DESCRIPTION open reading frames, and features. It allows complete DESCRIPTION restriction enzyme analysis including user defined enzymes, DESCRIPTION enzyme filtering by overhang and cutting frequency, and a DESCRIPTION databases of over 300 enzymes. Motif analysis automatically DESCRIPTION locates motifs such as TACCC-binding and T-antigen sequences DESCRIPTION and supports user defined motifs. ORF analysis locates all DESCRIPTION open reading frames in both the sense and anti-sense DESCRIPTION direction. Start and stop codons are editable allowing DESCRIPTION support of mitochondrial codon tables. Features from GenBank DESCRIPTION files are automatically read and shown on the plasmid. DESCRIPTION DESCRIPTION In addition to automatic analysis, enzymes, motifs, and DESCRIPTION features can be added manually. The user can set position, DESCRIPTION font, and color. Default styles can be set and modified. DESCRIPTION Styles can be copied and pasted between objects. Plasmids DESCRIPTION can be output in Windows bitmap or Mac PICT formats, or cut DESCRIPTION and pasted through the clipboard. AUTHOR PREMIER Biosoft International RT - ADDRESS 3786 Corina Way ADDRESS Palo Alto, CA 94303-9504 ADDRESS U.S.A. CONTACT sales@PremierBiosoft.com SITE WWW Server at URL http://www.PremierBiosoft.com OS Windows 95, Windows 98, Windows NT LANGUAGE C++ VOLUME 1.4 MB REQUIRES - COMMENTS Commercial product, fully functional demo available at COMMENTS http://www.PremierBiosoft.com page. AC BC00542 NAME Spectrum DOMAIN Sequence analysis DOMAIN Phylogeny DESCRIPTION SPECTRUM is a new Macintosh. and Microsoft. Windows. program DESCRIPTION designed to read in phylogenetic 4-state or binary data in DESCRIPTION NEXUS format, and display the bipartition spectra DESCRIPTION corresponding to the data. DESCRIPTION It can also be used to find the tree whose expected spectrum DESCRIPTION is closest to the observed spectrum (the "closest tree"). DESCRIPTION SPECTRUM outputs spectra in Microsoft. Excel format as DESCRIPTION tab-delimited text files and trees as TREEVIEW files. AUTHOR Michael A. Charleston, Roderic D. M. Page RT - ADDRESS Graham Kerr Building, ADDRESS D.E.E.B., ADDRESS I.B.L.S., ADDRESS University of Glasgow, ADDRESS Glasgow G12 8QQ, ADDRESS Scotland, U.K. CONTACT m.a.charleston@bio.gla.ac.uk SITE WWW Server at URL http://taxonomy.zoology.gla.ac.uk/mike/spectrum/spectrum.html OS MacOS, Microsoft. Windows '95/NT LANGUAGE C++ VOLUME approx. 600 kbytes REQUIRES 8 Mbytes RAM COMMENTS This is a beta-version: any comments, suggestions and COMMENTS problems should be sent to Mike Charleston at the e-mail COMMENTS address given. COMMENTS It is free but please register it so I can keep users up to COMMENTS date with new releases and bug fixes. AC BC00552 NAME ESSA DOMAIN Sequence display DOMAIN Sequence analysis DOMAIN RNA analysis DOMAIN WWW server DESCRIPTION With ESSA, we propose an approach of RNA secondary DESCRIPTION structure analysis based on extensive viewing within a DESCRIPTION friendly graphical interface. This computer program is DESCRIPTION organized around the display of folding models produced by DESCRIPTION two complementary methods suitable to draw long RNA DESCRIPTION molecules. Any feature of interest can be managed directly DESCRIPTION on the display and highlighted by a rich combination of DESCRIPTION colours and symbols with emphasis given to structural probe DESCRIPTION accessibilities. ESSA also includes a word searching DESCRIPTION procedure allowing easy visual identification of structural DESCRIPTION features even complex and degenerated. Analysis functions DESCRIPTION make it possible to calculate the thermodynamic stability DESCRIPTION of any part of a folding using several models and compare DESCRIPTION homologous aligned RNA both in primary and secondary DESCRIPTION structure. The predictive capacities of ESSA which brings DESCRIPTION together the experimental, thermodynamic and comparative DESCRIPTION methods, are increased by coupling it with a program DESCRIPTION dedicated to RNA folding prediction based on constraints DESCRIPTION management AUTHOR Chetouani F., Monestie P., Thebault P., Gaspin C., Michot B. RA Chetouani F., Monestie P., Thebault P., Gaspin C., Michot B.; RT "ESSA: An integrated and interactive computer tool for RT analysing RNA secondary structure."; RL Nucleic Acids Res 25(17):3514-3522(1997). ADDRESS Gaspin : Station de Biometrie et d'Intelligence Artificielle, ADDRESS I.N.R.A., Chemin de Borde-Rouge, Auzeville BP 27, 31326 ADDRESS Castanet-Tolosan Cedex, FRANCE ADDRESS tel : (33) 05 61 28 52 82; fax : (33) 05 61 28 53 35; ADDRESS e-mail : gaspin@toulouse.inra.fr ADDRESS Michot, Chetouani ADDRESS Laboratoire de Biologie Moleculaire Eucaryote du C.N.R.S., ADDRESS Universite Paul Sabatier, 118 route de Narbonne, ADDRESS 31062 Toulouse Cedex, FRANCE ADDRESS tel : (33) 05 61 33 58 65; fax : (33) 05 61 33 58 86; ADDRESS e-mail : bmichot@ibcg.biotoul.fr farid@ibcg.biotoul.fr CONTACT essa@toulouse.inra.fr SITE WWW Server at URL http://www-bia.inra.fr/T/essa/Doc/essa_home.html OS UNIX : SUN, SGI, HP LANGUAGE C VOLUME 200 Kb REQUIRES - AC BC00558 NAME TEST_SHOTGUN DOMAIN Sequence analysis DOMAIN Genome Analysis DESCRIPTION TEST_SHOTGUN is a Fortran program which DESCRIPTION DESCRIPTION simulates a shotgun sequencing project. It is a handy tool DESCRIPTION for estimating not only how much work must be done (or DESCRIPTION remains to be done) for a given project, but also how much DESCRIPTION it will cost. It simulates projects up to 1 Mbp directly in DESCRIPTION memory. For projects larger than that it simulates it in 1 DESCRIPTION Mbp region and then scales the results. It is known to DESCRIPTION compile and run on OpenVMS, Digital Unix, and IRIX. DESCRIPTION Probably it will work on other platforms, or at most, DESCRIPTION require only minimal code changes. AUTHOR David Mathog RT - ADDRESS - CONTACT mathog@seqaxp.bio.caltech.edu SITE WWW Server at URL http://seqaxp.bio.caltech.edu/www/test_shotgun.html OS OpenVMS, Digital Unix, and IRIX LANGUAGE Fortran VOLUME - REQUIRES Fortran compiler AC BC00559 NAME ANNHYB DOMAIN Sequence analysis DESCRIPTION Annhyb is a free little software (for Windows 95 with a DESCRIPTION very simple user interface) that is able to calculate DESCRIPTION various DNA sequence (degenerated or not) parameters: DESCRIPTION Melting temperature (nearest neighbors algorihtm) DESCRIPTION Molar extinction coefficient DESCRIPTION Molecular weight DESCRIPTION Reverted and complemented sequence DESCRIPTION IUPAC compliant sequence AUTHOR O. Friard, G. Stefanuto RA Rychlik W., Spencer W.J. and Rhoads D.E.; RT "Optimization of the annealing temperature for DNA RT amplification in vitro."; RL Nucleic Acids Res. 18(21):6409-6412(1990). RA Breslauer K.J., Frank R., Blocker H. and Marky L.A.; RT "Predicting DNA duplex stability from the base RT sequence."; RL Biochemistry 83:3746-3750(1986). ADDRESS O. Friard ADDRESS Dipartimento di Genetica, Biologia e Biochimica ADDRESS via Santena, 5bis ADDRESS I-10126 TURIN ADDRESS ITALY CONTACT friard@molinette.unito.it SITE WWW Server at URL http://130.192.126.18/programs.html OS windows 95/98/NT 4.0 LANGUAGE - VOLUME - REQUIRES - AC BC00560 NAME Alkami Expert for PCR DOMAIN Sequence analysis DOMAIN Genetic tools DOMAIN WWW server DOMAIN Statistical significance SERVER http://www.alkami.com DESCRIPTION A PCR (polymerase chain reaction)design, troubleshooting and DESCRIPTION optimization tool. Alkami PCR integrates PCR reference DESCRIPTION resources and statistical tools with a simple interface. AUTHOR - RT - ADDRESS Alkami Biosystems ADDRESS P.O. Box 11216 ADDRESS Berkeley, CA 94712-2216 CONTACT info@alkami.com SITE WWW Server at URL http://www.alkami.com OS - LANGUAGE - VOLUME - REQUIRES - COMMENTS This is a FREE online service intended to introduce COMMENTS molecular biologists to a powerful PCR optimization tool. AC BC00566 NAME CloneIt DOMAIN Sequence analysis DOMAIN Sequence tools DOMAIN Restriction maps DESCRIPTION Molecular biologists often have to sub-clone DESCRIPTION plasmidic vectors: a DNA plasmid is cleaved and ligated DESCRIPTION with an exogen DNA fragment previously excised from an DESCRIPTION other plasmid. The necessary cuts are made by restriction DESCRIPTION enzymes which then must be carefully choosen in order to DESCRIPTION minimize the steps required to obtain the desired DESCRIPTION molecule. During the selection of those enzymes, the main DESCRIPTION difficulties encountered come from the knowldege of: DESCRIPTION the enzymes' characteristics DESCRIPTION the localization of the cuts within the sequence DESCRIPTION the complementarity between the protuding ends DESCRIPTION the possible self ligation of the vector DESCRIPTION the use of modifying DNA polymerases that generate blunt ends DESCRIPTION the constraint to clone the insert in-frame with a vector sequence DESCRIPTION the use of partial digestions DESCRIPTION the creation of a stop codon after the ligation. DESCRIPTION This exercise takes a long time even with a DESCRIPTION computorized help of the classic DNA analysis softwares, DESCRIPTION such as "DNA Strider" , that only help the user by DESCRIPTION localizing restriction sites that are present a few times DESCRIPTION in a plasmid sequence. All combinations cannot be humanly DESCRIPTION checked by the scientist, so a simple cloning strategy can DESCRIPTION be missed by the experimenter. DESCRIPTION The program is not an expert system, as it does not "learn" DESCRIPTION the logical steps accomplished by the biologist and it does DESCRIPTION not have to be accompanied in its search: it just runs an DESCRIPTION algorithm that explores all the possible enzymes DESCRIPTION combinations that could be used to clone the molecules. DESCRIPTION This program called CloneIt , written in ANSI C, provides a DESCRIPTION useful aid for any molecular biologist who wants to quickly DESCRIPTION find sub-cloning, in-frame deletions, frameshifts DESCRIPTION strategies, which would otherwise be difficult to DESCRIPTION discover. This program handle parameters such as DESCRIPTION usage of a phosphatase (CIP) DESCRIPTION usage of modifying polymerases that blunt overhanged ends DESCRIPTION partial digestions DESCRIPTION 5' or/and 3' in-frame ligation DESCRIPTION digestion post ligation DESCRIPTION digestion to direct insert DESCRIPTION detection of stop codon after ligation DESCRIPTION Compare 2 sequences from the point of view of restriction sites. DESCRIPTION Display a restriction map. DESCRIPTION Translation of restriction enzymes databases. DESCRIPTION Management of large cloning projects. AUTHOR Pierre LINDENBAUM RA Lindenbaum P.; RT "CloneIt: finding cloning strategies, in-frame deletions and RT frameshifts."; RL Bioinformatics 14(5):465-466(1998). ADDRESS Pierre LINDENBAUM. ADDRESS Laboratoire de Biologie Moleculaire des Rotavirus. ADDRESS Virologie et Immunologie Moleculaires. ADDRESS Institut National de la Recherche Agronomique. ADDRESS 78350 Jouy-en-Josas Cedex FRANCE. CONTACT lindenb@biotec.jouy.inra.fr SITE WWW Server at URL http://locus.jouy.inra.fr/soft/cloneit/cloneit.html OS UNIX, MAC, PC LANGUAGE ANSI-C VOLUME about 200 Ko REQUIRES C compilator (works with GCC) COMMENTS I would like to thank Audrey Nepveu-de-Villemarceau, COMMENTS Janine L., Dr S. Hazout and his team, Philippe Bessieres, COMMENTS Christine Young, and Maria Piron for their help. AC BC00570 NAME RASA 2.2 DOMAIN Sequence analysis DOMAIN Structure prediction DOMAIN Pattern Identification DOMAIN Phylogeny DOMAIN Statistical significance DOMAIN Comparative analysis DESCRIPTION RASA 2.2 provides a set of tools for measuring DESCRIPTION phylogenetic signal and for studying its distribution DESCRIPTION among taxa. DESCRIPTION DESCRIPTION This software is used for DESCRIPTION * measuring signal DESCRIPTION * testing the suitability of available outgroup taxa DESCRIPTION * detecting long branches in the taxon variance plot DESCRIPTION * performing the mixed-character taxon test for differential DESCRIPTION lineage sorting DESCRIPTION * performing bootstrap power and effect to examine the DESCRIPTION power curve for your data. DESCRIPTION DESCRIPTION Exploratory options include DESCRIPTION * determining the signal spectrum for a set of sequences DESCRIPTION * removing noisy sites DESCRIPTION DESCRIPTION Some researchers have used the software to examine DESCRIPTION hypotheses of alignment using phylogenetic signal as the DESCRIPTION criterion. DESCRIPTION DESCRIPTION This software can be used on discrete data (molecular, DESCRIPTION morphological, or mixed). AUTHOR James Lyons-Weiler, PhD RA Lyons-Weiler, J., Hoelzer, G.A. and Tausch R.J.; RT "Relative Apparent Synapomorphy Analysis (RASA) I: RT the statistical measurement of phylogenetic signal."; RL Molecular Biology and Evolution 13:749-757(1996). RA Lyons-Weiler, J. and Milinkovitch, M.C.; RT "A phylogenetic approach to the problem of differential RT lineage sorting."; RL Molecular Biology and Evolution 14:968-975(1997). RA Lyons-Weiler, J. and Hoelzer, G.A.; RT "Escaping from the Felsenstein Zone by detecting long RT branches in phylogenetic data."; RL Molecular Phylogenetics and Evolution 8:375-384(1997). RA Lyons-Weiler, J. and Hoelzer, G.A.; RL "Optimal outgroup analysis."; RL Biological Journal of the Linnean Society 64:493(1998). RA Milinkovitch, M.C. and Lyons-Weiler, J.; RT "Finding optimal outgroup topologies and convexities RT when the choice of outgroups is not obvious."; RL Molecular Phylogenetics and Evolution 9:348-357(1998). ADDRESS - CONTACT jfl8@psu.edu SITE WWW Server at URL http://test1.bio.psu.edu/LW/list.htm OS Mac/PowerPC REQUIRES All superfluous extensions off. COMMENTS The software will be updated and bugs fixed at COMMENTS irregular intervals. Watch for updates. AC BC00571 NAME Redasoft Plasmid 1.0 DOMAIN Sequence analysis DOMAIN Sequence tools DOMAIN Genetic and Physical Mapping DOMAIN Restriction maps DESCRIPTION Redasoft Plasmid 1.0 is an exciting new software tool DESCRIPTION designed to to help life scientists draw high quality DESCRIPTION (circular or linear) vector maps (with or without sequence) DESCRIPTION and perform DNA sequence analysis quickly and easily. DESCRIPTION DESCRIPTION Plasmid includes revolutionary new features such as an DESCRIPTION integrated web browser and the ability to automatically DESCRIPTION parse Genbank and EMBL / VectorDB files and display them as DESCRIPTION fully labeled graphical maps! DESCRIPTION DESCRIPTION Plasmid includes a database of nearly 1000 enzymes, support DESCRIPTION for multiple swquence file formats and a custom restriction DESCRIPTION enzyme list. AUTHOR Redasoft RT - ADDRESS - CONTACT info@redasoft.com SITE WWW Server at URL http://www.redasoft.com OS Windows 95/98/NT LANGUAGE C++ VOLUME 2 MB REQUIRES - AC BC00572 NAME WWW2GCG DOMAIN GCG tools DOMAIN Sequence analysis DESCRIPTION WWW interface to GCG package AUTHOR Marc Colet RA Colet M., Herzog R.; RT "WWW2GCG, a web interface to the GCG biological sequences RT analysis software"; RL Comput. & Graphics 20:445-450(1996). ADDRESS BEN ADDRESS Rue des Chevaux 67, 1640 Rhode-Saint-Genese, BELGIUM CONTACT mcolet@dbm.ulb.ac.be SITE ftp anonymous ftp.be.embnet.org SITE Directory /pub/www2gcg SITE-CONTACT gbottu@dbm.ulb.ac.be OS Solaris, DEC UNIX,SGI IRIX LANGUAGE C,Perl, JavaScript, Java VOLUME - REQUIRES GCG v9, WWW server, Perl v5 COMMENTS contains sequence editor Java applet : ROASTED COMMENTS displays graphics using licenced GIF driver or COMMENTS (included in distribution) Fig2Java of Hayashi & Miyajima NAME K-Estimator 4.3 DOMAIN Sequence analysis DOMAIN Sequence tools DOMAIN Molecular Evolution DESCRIPTION K-Estimator is a computer program for estimating the number DESCRIPTION of nucleotide substitutions per site (synonymous, Ks, and DESCRIPTION nonsynonymous, Ka, for coding regions, and overall, K, for DESCRIPTION noncoding regions) and the confidence intervals of these DESCRIPTION estimates obtained by Monte-Carlo simulations. For DESCRIPTION noncoding regions, K can be estimated by applying several DESCRIPTION methods to correct for multiple-hits (Jukes and Cantor, DESCRIPTION Kimura-2p, Tajima and Nei, Tajima 1-, 2-, and 3-p). For DESCRIPTION coding regions Ks and Ka are estimated based on the method DESCRIPTION described in Comeron (1995). AUTHOR Josep M. Comeron RA Comeron, J.M.; RT "A method for estimating the numbers of synonymous RT and nonsynonymous substitutions per site"; RL J. Mol. Evol. 41:1152-1159(1995). ADDRESS Dep. Ecology and Evolution ADDRESS University of Chicago ADDRESS 1101 east 57th St. ADDRESS Chicago, IL 60637, USA CONTACT jcomeron@midway.uchicago.edu SITE WWW Server at URL http://mk-dimension-1.uchicago.edu OS PC LANGUAGE Visual Basic 5 VOLUME 3 Mb REQUIRES Windows 95/98/NT AC BC00577 NAME NetPrimer DOMAIN Sequence editor DOMAIN Sequence analysis DOMAIN Sequence tools DOMAIN Oligomer design and synthesis DESCRIPTION NetPrimer is a web-based program that analyzes individual or DESCRIPTION pairs of primers. It is available free of charge. DESCRIPTION The program combines the latest primer design algorithms DESCRIPTION with an intuitive interface allowing the user to quickly DESCRIPTION analyze primers. Primers are analyzed for melting temperature DESCRIPTION using the nearest neighbor thermodynamic theory to ensure DESCRIPTION accurate Tm prediction. Primers are analyzed for all DESCRIPTION secondary structures including hairpins, self-dimers, and DESCRIPTION cross-dimers in primer pairs. This analysis ensures DESCRIPTION the availability of the primer for the reaction as well as DESCRIPTION minimizing the formation of primer dimer. DESCRIPTION The program eases quantitation of primers by calculating DESCRIPTION primer molecular weight and optical activity. DESCRIPTION To facilitate the selection of an optimal primer, DESCRIPTION each primer is given a rating based on the stability of its DESCRIPTION secondary structures. Extensive help including algorithms DESCRIPTION and formulae used is available online. A complete analysis DESCRIPTION report can be printed for individual primers or primer pairs. AUTHOR PREMIER Biosoft International RT - ADDRESS 3786 Corina Way, Palo Alto, CA 94303-4504 ADDRESS Tel: 650-856-2703, Fax: 650-843-1250 CONTACT support@PremierBiosoft.com SITE WWW Server at URL www.PremierBiosoft.com/NetPrimer.html OS Windows 95, Windows 98, Windows NT LANGUAGE Java, Javascript VOLUME 1.8 MB REQUIRES - COMMENTS This appears to be the most comprehensive, free primer analysis COMMENTS program available on the Internet. AC BC00587 NAME BioEdit DOMAIN Sequence format conversion tools DOMAIN Sequence display DOMAIN Sequence editor DOMAIN Sequence analysis DOMAIN RNA analysis DOMAIN Alignment editing and display DOMAIN Alignment browser DOMAIN Searching databases DOMAIN General tools DESCRIPTION BioEdit is a user-friendly, graphically-oriented sequence DESCRIPTION alignment editor for Windows 95/98/NT. Features include DESCRIPTION several modes of hand alignment, auto-linking to ClustalW, DESCRIPTION user-defined color view (editable by mouse point- and DESCRIPTION click), separate amino acid and nucleotide color tables, DESCRIPTION Shaded views with many options, RNA comparative analysis DESCRIPTION tools (including mutual information with interactive 2-D DESCRIPTION matrix plots and area plots), restriction mapping, browsing DESCRIPTION restriction enzymes by company, easy plasmid drawing and DESCRIPTION annotation, protein hydropathy plots, can handle very large DESCRIPTION alignments (up to 20000 sequences of undefined length), DESCRIPTION several translation modes, nucleotide/translation toggling DESCRIPTION for alignment in both protein and DNA views, 6-frame DESCRIPTION translations, basic sequence manipulations (complement, DESCRIPTION reverse, uppercase, lowercase), internal web browser (HTML DESCRIPTION 2.0-compliant), auto-link to external browser with internet DESCRIPTION bookmarks, on-line help system, configure external apps via DESCRIPTION a graphical interface to automatically run through a DESCRIPTION BioEdit interface, split-window views for editing of two DESCRIPTION different places in an alignment at the same time, local DESCRIPTION NCBI BLAST accessories, single sequence editing and DESCRIPTION manipulation, retains GenBank data (eg, FEATURES, DESCRIPTION REFERENCE, SOURCE, PID or NID, etc), binary file format for DESCRIPTION fast save/open of very large files (alignments up to 100 Mb DESCRIPTION and more are no problem), correct spacing of all available DESCRIPTION fonts in edit window and in shaded view, creation of DESCRIPTION high-quality alignment figures via shading with many DESCRIPTION options (including full-color, id/sim shading, enhanced DESCRIPTION metafile copy and paste directly into graphics programs), DESCRIPTION easy formatted text print preview. AUTHOR Tom Hall RT - ADDRESS Department of Microbiology, ADDRESS North Carolina State University ADDRESS Raleigh, NC 27695 CONTACT tahall2@unity.ncsu.edu SITE WWW Server at URL http://www.mbio.ncsu.edu/RNaseP/info/programs/BIOEDIT/bioedit.html OS Windows LANGUAGE - VOLUME BioEdit.zip file = 7.6 Mb REQUIRES Windows 95, 98 or NT, Pentium 60+, 16 Mb RAM+, REQUIRES 20 Mb hard drive space AC BC00589 NAME DNATools DOMAIN Sequence analysis DESCRIPTION Software package for analysis of DNA and protein sequences. DESCRIPTION In addition to basic functions, the package supports unattended DESCRIPTION blast mail search and data retrieval, creation of searchable DESCRIPTION data bases for blast searching, clustalw multi-sequence DESCRIPTION alignment, advanced search functions, free text search on DESCRIPTION sequence headers, a number of functions for managing smal DESCRIPTION (4-8000) EST projects, a full set of functions for handling DESCRIPTION and analysis of SAGE data, primer design and mail ordering. AUTHOR Soeren W. Rasmussen RT - ADDRESS Carlsberg Laboratory ADDRESS Department of Physiology ADDRESS 10 Gl. Carlsbergvej ADDRESS Copenhagen ADDRESS DK-2500 ADDRESS Denmark CONTACT swr@crc.dk SITE WWW Server at URL http://www.crc.dk/phys/A01B04_dnatools.htm OS Windows 95/98/NT LANGUAGE English VOLUME - REQUIRES - AC BC00591 NAME K-Estimator 5.0 DOMAIN Sequence analysis DOMAIN Sequence tools DOMAIN Molecular Evolution DESCRIPTION K-Estimator is a computer program for estimating the number DESCRIPTION of nucleotide substitutions per site (synonymous [Ks], and DESCRIPTION nonsynonymous [Ka], for coding regions, and overall [K], for DESCRIPTION noncoding regions) and the confidence intervals of these DESCRIPTION estimates obtained by Monte-Carlo simulations. DESCRIPTION Divergence Estimates: For noncoding regions, the program can DESCRIPTION estimate the overall (K) number of nucleotide substitutions DESCRIPTION per site using several multiple-hits at a site correcting DESCRIPTION methods: Jukes and Cantorīs 1-parameter (Jukes and Cantor, 1969), DESCRIPTION Kimuraīs 2-p(Kimura, 1980), Tajima and Nei (Tajima and Nei, 1984), DESCRIPTION and Tajimaīs 1-p, 2-p and 4-p (Tajima, 1993). DESCRIPTION When coding regions are under analysis, K-Estimator 5.0 applies DESCRIPTION the method described in Comeron (1995) to estimate Ks and Ka. DESCRIPTION This method is a modification of Li's (1993) and Pamilo and DESCRIPTION Bianchi's (1993)(LPB) method that better quantifies the actual DESCRIPTION number of transitions and transversions and reduces stochastic DESCRIPTION errors (see Comeron, 1995, for details and comparison to previous DESCRIPTION methods). Three genetic codes can be applied: Universal, DESCRIPTION Vertebrate mitochondrial, or Drosophila mitochondrial. DESCRIPTION Furthermore, three different options can be applied to restrict DESCRIPTION the codons that are under analysis. DESCRIPTION Confidence Intervals: K-Estimator 5.0 obtains the Confidence DESCRIPTION Intervals (C.I.) of divergence estimates (K for noncoding regions, DESCRIPTION and Ks and Ka for coding regions) by Monte Carlo simulations. DESCRIPTION Computer simulations take into account the following parameters: DESCRIPTION 1)Divergence Value; K or Ks and Ka, 2)number of nucleotides or DESCRIPTION codons, 3)the transition : transversion (alfa:beta) substitution DESCRIPTION ratio, and 4) the G+C content for noncoding regions, and the DESCRIPTION amino acid composition and G+C content at the third position of DESCRIPTION codons for coding regions. The program can also calculate the DESCRIPTION exact probability of obtaining any particular divergence value DESCRIPTION (K for noncoding regions, and Ks, Ka, and Ka/Ks for coding DESCRIPTION regions). DESCRIPTION K-Estimator 5.0 also obtain the expected distribution of the ratio DESCRIPTION Ka/Ks that has been classically applied to detect the action of DESCRIPTION positive selection (Ka/Ks>1). In particular, the program generates DESCRIPTION a condition where the number of nonsynonymous substitutions per DESCRIPTION nonsynonymous site (Ka) is on average equal to the value estimated DESCRIPTION for Ks, taking into account all the previous parameters from the DESCRIPTION analyzed pair of sequences. Therefore, it is obtained the null DESCRIPTION distribution and C.I. for Ks, Ka and, more important, for the DESCRIPTION ratio Ka/Ks, when the expectation (null hypothesis) for Ka/Ks is =1. AUTHOR Josep M. Comeron RA Comeron, J.M.; RT "A method for estimating the numbers of synonymous and RT nonsynonymous substitutions per site"; RL J. Mol. Evol. 41:1152-1159(1995). RA Comeron, J.M.; RT "K-Estimator: Calculation of the number of nucleotide RT substitutions per site and the confidence intervals"; RL Bioinformatics (1999, in press). ADDRESS Dep. Ecology and Evolution ADDRESS University of Chicago ADDRESS 1101 east 57th St. ADDRESS Chicago, IL 60637, USA CONTACT jcomeron@midway.uchicago.edu SITE WWW Server at URL http://mk-dimension-1.uchicago.edu OS PC LANGUAGE Visual Basic 5 VOLUME 3 Mb REQUIRES Windows 98/NT AC BC00593 NAME pDRAW32 DOMAIN Sequence display DOMAIN Sequence editor DOMAIN Sequence analysis DOMAIN Restriction maps DESCRIPTION Freeware software for various forms of DNA analysis, DESCRIPTION virtual DNA cloning, graphics generation, DESCRIPTION PCR temperature calculation, XY-dotblots and more. AUTHOR Kjeld Olesen, Acaclone Software RT - ADDRESS - CONTACT Kjeld Olesen, acaclone@hotmail.com SITE WWW Server at URL http://www2.crosswinds.net/~acaclone OS Windows 95 or newer LANGUAGE - VOLUME 3 MB REQUIRES - AC BC00596 NAME SimPlot DOMAIN Sequence analysis DOMAIN Protein sequence analysis DOMAIN Molecular Evolution DOMAIN Statistical significance DESCRIPTION SimPlot is a graphical program for analysis of sequences DESCRIPTION (e.g. HIV) suspected of being recombinant. The program DESCRIPTION recognizes multiple file formats, and sequences can be DESCRIPTION analyzed individually or as members of groups. Three DESCRIPTION major methods are available: similarity/diversity plots, DESCRIPTION bootscanning, and informative site analysis. Results DESCRIPTION can be printed, copied to the Windows clipboard, or DESCRIPTION saved as a graphics metafile. The author reserves DESCRIPTION copyright, but the software is provided at no cost. AUTHOR Stuart C. Ray, M.D. RA Lole K.S., Bollinger R.C., Paranjape R.S., Gadkari D., RA Kulkarni S.S., Novak N.G., Ingersoll R., Sheppard H.W., and Ray S.C.; RT "Full-Length Human Immunodeficiency Virus Type 1 Genomes RT from Subtype C-Infected Seroconverters in India, with RT Evidence of Intersubtype Recombination"; RL J Virol 73:152-160 (1999). ADDRESS Stuart C. Ray, M.D. ADDRESS Division of Infectious Diseases ADDRESS Johns Hopkins University School of Medicine ADDRESS 720 Rutland Avenue, Ross 1159 ADDRESS Baltimore, MD 21205 CONTACT sray@jhmi.edu SITE WWW Server at URL http://www.med.jhu.edu/deptmed/sray/download/ OS Windows 95, Windows 98, Windows NT LANGUAGE Pascal (Borland Delphi) VOLUME 1.2 MB REQUIRES 32-bit PHYLIP (phylip95.exe) AC BC00597 NAME NHGRI's WebBLAST DOMAIN Sequence analysis DOMAIN Protein sequence analysis DOMAIN Alignment browser DESCRIPTION WebBLAST 2.0 is a suite of Macintosh and UNIX programs intended to DESCRIPTION assist in organizing sequencing data as well as providing first-pass DESCRIPTION sequence analysis in an automated fashion. One of the main features of DESCRIPTION WebBLAST is that its system requirements are minimal, needing only DESCRIPTION MacPerl on the Macintosh client, Perl 5.004 and BLAST on the UNIX DESCRIPTION client, and a Web server. All output is viewed through a Web browser, DESCRIPTION allowing users to access the refined data regardless of platform. The DESCRIPTION software can be previewed and downloaded at DESCRIPTION http://genome.nhgri.nih.gov/webblast. DESCRIPTION DESCRIPTION Data enters the WebBLAST pipeline through the use of a MacPerl droplet DESCRIPTION on the Macintosh connected to the sequencer. The droplet transfers the DESCRIPTION data into the UNIX file system and places the data into a holding area DESCRIPTION on the server. A nightly cron job then invokes the automatic processing DESCRIPTION of new data: [1] Sequences are moved from the holding area to the DESCRIPTION appropriate directory within the UNIX file system. [2] Sequences are DESCRIPTION screened for the presence of vector, alu, and other repetitive DESCRIPTION sequences and masked. [3] Local BLAST searches are then run on the DESCRIPTION masked data, assessing each BLAST hit for statistical significance. [4] DESCRIPTION A CGI program generates HTML pages presenting the user with a summary DESCRIPTION table of hit counts as well as information on the significant hits. [5] DESCRIPTION Sequence data are re-BLASTed monthly against the NCBI month database, DESCRIPTION with any new hit information being appended to the summary pages of the DESCRIPTION appropriate sequence set; this assures that BLAST results are kept DESCRIPTION up-to-date. DESCRIPTION Once the sequence comparisons have been run, users can add comments to DESCRIPTION individual sequences that can be viewed by all users. Users can also DESCRIPTION view the associated sequence traces directly through the use of a Java DESCRIPTION applet. Each data set can be password protected, so that multiple DESCRIPTION projects can be supported while maintaining the integrity and security DESCRIPTION of the data. Data can be exported for use with assembly programs such DESCRIPTION as the PHRED/PHRAP/CONSED. As the programs are written in perl, users DESCRIPTION can easily modify the scripts to include additional analyses, such as DESCRIPTION performing BLAST runs against in-house data sets. AUTHOR Joseph Ryan, Erik Ferlanti, Izabela Makalowska, Andreas D. AUTHOR Baxevanis RT - ADDRESS - CONTACT webblaster@nhgri.nih.gov SITE WWW Server at URL http://genome.nhgri.nih.gov/webblast/ OS Unix LANGUAGE - VOLUME - REQUIRES NHGRI::Blastall, Perl AC BC00601 NAME Jalview DOMAIN Sequence display DOMAIN Sequence analysis DOMAIN Protein sequence analysis DOMAIN Alignment editing and display DOMAIN Alignment browser DOMAIN JAVA DOMAIN Multivariate analysis DOMAIN WWW server SERVER http://circinus.ebi.ac.uk:6543/jalview DESCRIPTION A multiple sequence alignment viewer and editor. Alignments DESCRIPTION can be divided into subfamilies using a tree or by hand. DESCRIPTION Conservation can then be calculated using physico-chemical DESCRIPTION properties within subfamilies or across the whole alignment. DESCRIPTION Principal component analysis can also be used as an DESCRIPTION alternative way of clustering the sequences. An SRS server DESCRIPTION can be used to fetch and display the sequence features and DESCRIPTION any PDB structures listed. There is limited access to DESCRIPTION external programs including clustalw and jnet secondary DESCRIPTION structure prediction. AUTHOR Michele Clamp RT - ADDRESS The Sanger Centre ADDRESS Wellcome Trust Genome Campus ADDRESS Hinxton ADDRESS Cambs. ADDRESS CB10 1SA ADDRESS UK CONTACT michele@sanger.ac.uk SITE WWW Server at URL http://circinus.ebi.ac.uk:6543/jalview OS - LANGUAGE java1.1 VOLUME 300kb REQUIRES Java runtime environment