Catalogue of Molecular Biology Programs Release 6.1 23 Jul 1999 All thanks are in the file biocatal.thanks. ===================================================================== AC BC00175 NAME AACOMP DOMAIN Protein sequence analysis DESCRIPTION AACOMP is part of the fasta package DESCRIPTION calculate the amino acid composition and DESCRIPTION and molecular weight of a sequence. AUTHOR W. R. Pearson RT - ADDRESS U. of Virginia Dept. of Biochemistry CONTACT W. R. Pearson: wrp@virginia.edu SITE ftp anonymous ftp.virginia.edu SITE Directory /pub/fasta = fasta(version number) SITE-CONTACT W. R. Pearson wrp@virginia.edu OS - LANGUAGE - VOLUME - AC BC00176 NAME ANTHEPROT 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 Molecular modelling and graphics DESCRIPTION ANalyze THE PROTeins DESCRIPTION ANTHEPROT is a package that allow to make: DESCRIPTION * Study of physico-chemical properties: hydrophobicity, DESCRIPTION antigenicity, flexibility, solvent accessibility, DESCRIPTION amphiphilicity. DESCRIPTION * Secondary structure prediction: Chou & Fasman, Garnier, DESCRIPTION Gibrat, Deleage, Levin. DESCRIPTION * Prediction of transmembranous regions & of structural DESCRIPTION domains. DESCRIPTION * Multiple alignment : Method of Feng & Doolittle, Higgins, DESCRIPTION Needleman & Wunsch. DESCRIPTION * Search for biological sites using PROSITE, and PATMAT DESCRIPTION from J.C. Wallace & S.Henikoff. DESCRIPTION * Search for homologous protein : Program FASTA (W. Pearson) DESCRIPTION * Identity level between several sequences. DESCRIPTION * Look and handle protein structures from PDB DESCRIPTION * Tools: Editor, File, Printing, format, colors ... AUTHOR G. Deleage, C. Geourjon RA Geourjon C., Deleage G., Roux B.; RT "ANTHEPROT : An interactive graphic software for analyzing RT protein structures from sequences."; RL J. Mol. Graph. 9:188-190(1991). RX Medline; 92126617. RX SeqAnalRef; GEOC9101. RA Deleage G., Clerc F.C., Roux B., Gautheron D.C.; RT "ANTHEPROT: a package for protein sequence analysis using a RT microcomputer."; RL Comput. Appl. Biosci. 4:351-356(1988). RX Medline; 88327410. RX SeqAnalRef; DELG8801. RA Deleage G., Clerc F.F., Roux B.; RT "ANTHEPROT: IBM PC and Apple MacIntosh versions."; RL Comput. Appl. Biosci. 5:159-160(1989). RX Medline; 89248605. RX SeqAnalRef; DELG8901. RA Geourjon C., Deleage G.; RT "Interactive and graphic coupling between multiple alignments, RT secondary structure predictions and motif/pattern scanning RT into proteins."; RL Comput. Appl. Biosci. 9:87-91(1993). RX Medline; 93169503. RX SeqAnalRef; GEOC9301. RA Deleage G., Geourjon C.; RT "An interactive graphic program for calculating secondary RT structures content of proteins from circular dichroism spectrum."; RL Comput. Appl. Biosci. 9:197-199(1993). RX Medline; 93245049. RA Deleage G., Geourjon C.; RT "ANTHEPROT 2.0: A three-dimensional module fully coupled with RT protein sequence analysis methods."; RL J. Mol. Graph. 13:209-212(1995). ADDRESS Institut de Biologie et Chimie des Proteines ADDRESS IBCP-CNRS UPR 412, Groupe de modelisation et RMN ADDRESS 7, Passage du Vercors ADDRESS 69 367 Lyon cedex 07, FRANCE CONTACT deleage@ibcp.fr, geourjon@ibcp.fr SITE ftp anonymous ibcp.fr SITE Directory /pub/ANTHEPROT SITE-CONTACT geourjon@ibcp.fr or deleage@ibcp.fr SITE WWW server at URL http://www.ibcp.fr SITE-CONTACT geourjon@ibcp.fr or deleage@ibcp.fr OS Unix, DOS, Windows95 LANGUAGE fortran, C, Visual Basic VOLUME from 8 to 30 Mo REQUIRES IBM rs6000 with a 3D card and graPHIG's installed COMMENTS 3 versions available: COMMENTS * 1 for IBMrs6000 the most powerful one COMMENTS * A Windows version COMMENTS * A DOS version COMMENTS * A multi-platform is planned for 1996 AC BC00177 NAME BLOCKSEARCH DOMAIN Protein sequence analysis DESCRIPTION Functional analysis of protein sequences with DESCRIPTION scoring matrices derived from the BLOCKS DESCRIPTION database AUTHOR Fuchs R. (rf11522@glaxo.com) RA Fuchs R.; RT "Block searches on VAX and Alpha computer systems."; RL Comput. Appl. Biosci. 9(5):587-591(1993). RX Medline; 94123145. RX SeqAnalRef; FUCR9302. ADDRESS Glaxo Research Institute, 5 Moore Drive, Research Triangle Park, ADDRESS NC 27709, USA CONTACT rf11522@glaxo.com 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 OpenVMS, UNIX LANGUAGE C VOLUME - AC BC00178 NAME GREASE DOMAIN Protein sequence analysis DESCRIPTION Kyte-Doolittle hydropathicity profile AUTHOR Pearson W.R.; RA Kyte J., Doolittle R.F.; RT "A Simple Method for Displaying the Hydropathic Character of RT a Protein."; RL J. Mol. Biol. 157:105-132(1982). RX Medline; 82268984. RX SeqAnalRef; KYTJ8201. ADDRESS U. of Virginia Dept. of Biochemistry CONTACT William R. Pearson wrp@virginia.edu SITE ftp anonymous ftp.virginia.edu SITE Directory /pub/fasta = fasta(version number) SITE-CONTACT William Pearson wrp@virginia.edu OS all LANGUAGE - VOLUME - AC BC00179 NAME PKB DOMAIN Protein sequence analysis DESCRIPTION PKB is an object-oriented data base for protein three-dimensional DESCRIPTION structure, based on the S programming language. AUTHOR - RA Bryant S.H.; RT "PKB: A Program System and Data Base for Analysis RT of Protein Structure"; RL Proteins 5:233-247(1989). RX Medline; 89386632. RX SeqAnalRef; BRYS8901. ADDRESS - CONTACT - SITE ftp anonymous ncbi.nlm.nih.gov SITE Directory /pub/pkb SITE-CONTACT - OS - LANGUAGE - VOLUME - AC BC00181 NAME PRSTRC DOMAIN Protein sequence analysis DESCRIPTION MBCRR Software Package DESCRIPTION An implementation of the Chou-Fasman DESCRIPTION algorithm fo predicting protein secondary DESCRIPTION structures AUTHOR WW Ralph, T Webster, TF Smith, RA Ralph W.W., Webster T., Smith T.F.; RT "A modified Chou and Fasman protein structure algorithm."; RL Comput. Appl. Biosci. 3:211-216(1987). RX Medline; 88270157. RX SeqAnalRef; RALW8701. 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 FORTRAN VOLUME - AC BC00182 NAME RELATE DOMAIN Protein sequence analysis DESCRIPTION significance program described by Dayhoff DESCRIPTION (Atlas of Protein Sequence and Structure, DESCRIPTION Vol. 5, Supplement 3).Each chunk of 25 residues DESCRIPTION in one sequence is compared to every 25 DESCRIPTION residue fragment of the second sequence. DESCRIPTION Sequences which are genuinely related will DESCRIPTION have a large number of scores greater than DESCRIPTION 3 standard deviations above the mean score of DESCRIPTION all of the comparis AUTHOR William Pearson RT - ADDRESS U. of Virginia Dept. of Biochemistry CONTACT - SITE ftp anonymous ftp.virginia.edu SITE Directory /pub/fasta = fasta(version number) SITE-CONTACT William Pearson wrp@virginia.edu OS all LANGUAGE - VOLUME - AC BC00183 NAME SAPS DOMAIN Protein sequence analysis DESCRIPTION Statistical Analysis of Protein Sequences AUTHOR Volker Brendel RA Brendel V., Bucher P., Nourbakhsh I.R., Blaisdell B.E., Karlin S.; RT "Methods and algorithms for statistical analysis of protein sequences."; RL Proc. Natl. Acad. Sci. U.S.A. 89:2002-2006(1992). RX Medline; 92196045. RX SeqAnalRef; BREV9201. ADDRESS - CONTACT volker@gnomic.stanford.edu SITE ftp anonymous gnomic.stanford.edu SITE Directory /pub SITE-CONTACT Voker Brendel: volker@gnomic.stanford.edu OS UNIX LANGUAGE C VOLUME - AC BC00184 NAME Sensitive Sequence Comparison DOMAIN Protein sequence analysis DESCRIPTION Comparison of Proteins for Distance relationships AUTHOR - RT - ADDRESS EMBL CONTACT R. Rechid argos@embl.bitnet SITE - SITE-CONTACT - OS VAX/VMS Sun-3, Unix Sun-4, Unix LANGUAGE - VOLUME - AC BC00185 NAME TGREASE DOMAIN Protein sequence analysis DESCRIPTION graphic plot of Kyte-Doolittle profile AUTHOR William Pearson RT - ADDRESS U. of Virginia Dept. of Biochemistry CONTACT - SITE ftp anonymous ftp.virginia.edu SITE Directory /pub/fasta = fasta(version number) SITE-CONTACT William Pearson wrp@virginia.edu OS all LANGUAGE - VOLUME - AC BC00186 NAME VISA DOMAIN Protein sequence analysis DESCRIPTION VISA identifies amino acid patterns that are common to DESCRIPTION many members of a set of amino acid sequences, and dis- DESCRIPTION plays the distribution of common patterns along the se- DESCRIPTION quences in a series of histograms. Individual peaks of DESCRIPTION these histograms can be assigned different colors. Com- DESCRIPTION mon sequence patterns inherit and display the color of DESCRIPTION the peak in which they occur, leading to analogous seg- DESCRIPTION ments in the other sequences being marked in matching DESCRIPTION colors. These peaks usually correspond to the conserved DESCRIPTION sequence motifs that are characteristic of the studied DESCRIPTION proteins. The resulting color graphic overview of se- DESCRIPTION quence similarities can help to understand the architec- DESCRIPTION ture of the protein family and can be helpful while DESCRIPTION designing experiments to probe function. AUTHOR J. Posfai, Z. Szaraz and R.J.Roberts RA Posfai J., Szaraz Z., Roberts R.J.; RT "VISA: Visual Sequence Analysis for the comparison of RT multiple amino acid sequences"; RL Comp. Appl. Biosci. 10:537-544(1994). RX Medline; 95128958. RX SeqAnalRef; POSJ9401. ADDRESS Richard J. Roberts (or Janos Posfai) ADDRESS New England Biolabs, 32 Tozer Rd., Beverly, MA 01915. USA ADDRESS Tel: (1) 508-927-5054 CONTACT roberts@neb.com (posfai@neb.com) SITE ftp anonymous vent.neb.com SITE Directory /pub/software/visa SITE-CONTACT - OS Unix LANGUAGE C, Xview library VOLUME - REQUIRES Xview library AC BC00187 NAME WHAT-IF DOMAIN Protein sequence analysis DOMAIN Protein structure analysis DOMAIN Alignment Search software DOMAIN Molecular modelling and graphics DOMAIN Database and analysis DOMAIN Searching databases DESCRIPTION WHAT IF is an extensive protein DESCRIPTION modeling, protein structure analysis, DESCRIPTION database handler, molecular graphics package.It is DESCRIPTION available for all Silicon Graphics machines (from the DESCRIPTION Indigo all the way up to the 8 processor VGX machine). DESCRIPTION WHAT IF is also supported for the Bruker NMR spectrometer DESCRIPTION computers, DEC-alpha,-OSF SUN and for IBM-Pc (clones) DESCRIPTION running LINUX or DOS. The Pc version is distributed by a DESCRIPTION third party, but fully supported by us. A do-it-yourself DESCRIPTION version exists for IBM RS6000 machines. If really needed, DESCRIPTION WHAT IF can be made available for all Evans and Sutherland DESCRIPTION machines, but this will be an unsupported version. Contact DESCRIPTION me for special arrangements for such machines. The DESCRIPTION program costs $5000,-. Non-profit organisations pay DESCRIPTION $250,-. The program comes WITH source code (300.000 lines DESCRIPTION FORTRAN 77), WITH databases, and WITH extensive DESCRIPTION documentation (600 page writeup). There are no monthly DESCRIPTION fees. There are no strings attached to using WHAT IF. DESCRIPTION However, (re-)distribution is not allowed. There is NO DESCRIPTION service desk, and no guarantees are given. At present DESCRIPTION there are 240 installed sites world wide. A lisence is DESCRIPTION site-wide, and covers an unlimited number of workstations. DESCRIPTION Updates are send upon request and will cost $250,- to DESCRIPTION everybody. An update can be obtained as often as possible, DESCRIPTION and comes again with all data, writeup, etc. AUTHOR Gert Vriend RA Vriend G.; RT "WHAT IF: a molecular modelling and drug design program."; RL J. Mol. Graph. 8:52-56(1990). RX SeqAnalRef; VRIG9002. ADDRESS Gert Vriend ADDRESS EMBL, Meyerhofstrasse 1 ADDRESS D-69117 Heidelberg, Germany CONTACT vriend@EMBL-Heidelberg.DE SITE WWW Server at URL http://www.sander.embl-heidelberg.de/whatif/ OS UNIX, MSDOS LANGUAGE FORTRAN, C VOLUME Between 15-300MB (or up to 3GB) REQUIRES X windows or GL graphics for UNIX. COMMENTS We have seen WHAT IF working on: COMMENTS DEC ULTRIX, DEC ALPHA, PC Linux, PC DOS, SGI IRIX, IBM AIX, COMMENTS SUN SUNoS, SUN SOLARIS COMMENTS The original distribution can not be done via FTP, but source COMMENTS code updates can be done over FTP. Updates via FTP are free of COMMENTS costs. AC BC00359 NAME PROTEAN DOMAIN Protein sequence analysis DOMAIN Protein structure analysis DOMAIN Protein analysis tools DESCRIPTION PROTEAN finds structural motifs, beta sheets, alpha helices DESCRIPTION and turns, and plots hydrophobicity and charge, among DESCRIPTION other functions. A large library of analytical methods is DESCRIPTION available to predict protein structure. The software can also DESCRIPTION locate antigenic determinants and predict protease digestion DESCRIPTION patterns. The simple, elegant interface presents the most DESCRIPTION comprehensive suite of protein analysis tools available. AUTHOR - RT - ADDRESS DNASTAR, Inc. ADDRESS 1228 South Park Street ADDRESS Madison, WI 53715,U.S.A. ADDRESS Tel: +1-608-2587420, Fax: +1-608-2587439 CONTACT - sales@dnastar.com SITE - SITE-CONTACT - OS Win95/NT and MacIntosh LANGUAGE - VOLUME - REQUIRES LaserGene protein and DNA sequence analysis package COMMENTS Commercial software 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 BC00387 NAME PRATT DOMAIN Protein sequence analysis DOMAIN Pattern Identification DESCRIPTION Pratt is a program that allows the user to efficiently DESCRIPTION search for patterns conserved in a set of protein sequences. DESCRIPTION It allows the user to define the class of patterns to be DESCRIPTION searched for, and is then guaranteed to find all conserved DESCRIPTION patterns in this class. The time used by the program DESCRIPTION depends on the set of sequences, the class of patterns DESCRIPTION defined, and the minimum number of sequences a pattern DESCRIPTION is to match. Pratt can discover conserved patterns of the DESCRIPTION PROSITE type, including patterns with flexible wildcard DESCRIPTION regions and ambiguous positions. It can for example DESCRIPTION discover the pattern C-x(2,4)-C-x(3)-[ILVFYC]-x(8)-H-x(3,5)-H DESCRIPTION conserved in 240 unaligned zinc finger protein sequences DESCRIPTION (ZINC_FINGER_C2H2 in PROSITE). DESCRIPTION Version 2.1 announced February 1997 includes new functionality, DESCRIPTION patterns may be restricted to those matching a given sequence DESCRIPTION alignment, or a special query sequence. Heuristics and branch- DESCRIPTION and-bound have also been implemented making the program faster, DESCRIPTION especially for analysis of relativey similar sequences. New DESCRIPTION methods for scoring identified patterns have also been incoroporated. DESCRIPTION Version 2.1 has not been tested on VMS. AUTHOR Inge Jonassen RA Jonassen I., Collins J. F., Higgins D. G.; RT "Finding flexible patterns in unaligned protein sequences."; RL Protein Science (1995) 4:1587-159; RA Jonassen I.; RT "Efficient discovery of conserved patterns using a pattern graph."; RL subm. to CABIOS February 1997 ADDRESS Inge Jonassen, ADDRESS Dept. of Informatics, ADDRESS University of Bergen, ADDRESS HIB ADDRESS N5020 BERGEN ADDRESS NORWAY CONTACT Inge.Jonassen@ii.uib.no SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/unix SITE-CONTACT higgins@ebi.ac.uk SITE ftp anonymous ftp.ii.uib.no SITE Directory /pub/bio/Pratt SITE-CONTACT Inge.Jonassen@ii.uib.no OS UNIX,VMS,LINUX LANGUAGE ANSI C VOLUME 1 MByte diskspace REQUIRES at least 20Mbyte memory 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 BC00392 NAME BLASTPAT and FASTPAT DOMAIN Protein sequence analysis DOMAIN Alignment Search software DOMAIN WWW server DESCRIPTION Pattern Database Search Tools for Fast and Sensitive Gene DESCRIPTION Function Identification. DESCRIPTION BLASTPAT and FASTPAT are tools designed to identify protein DESCRIPTION sequences whose functions are not identified by standard BLAST DESCRIPTION or FASTA database searches. These modified versions of BLAST and DESCRIPTION FASTA perform rapid and sensitive searches of our Pattern DESCRIPTION Induced Multiple Alignment (PIMA) Pattern Database. The PIMA DESCRIPTION Pattern Database contains 22,422 patterns generated from DESCRIPTION multiple sequence alignments of 12,669 protein families we have DESCRIPTION identified in the NCBI's Entrez protein sequence database. DESCRIPTION Patterns in the PIMA database are encoded by a maximized DESCRIPTION information content alphabet. This extended alphabet includes DESCRIPTION the standard 20 letter IUPAC amino acid codes plus 61 other DESCRIPTION characters (lowercase characters, digits, other symbols) DESCRIPTION representing those combinations of residues which contribute the DESCRIPTION highest information as observed across all aligned positions in DESCRIPTION our protein family alignments. Pattern database searches are DESCRIPTION performed using new log-odds scoring matrices that we have DESCRIPTION developed for use with this new extended alphabet. In contrast DESCRIPTION to standard scoring matrices like PAM or BLOSUM, these new DESCRIPTION pattern-based matrices distinguish between conserved and DESCRIPTION variable positions, increasing search sensitivity and DESCRIPTION selectivity DESCRIPTION A more detailed description of these program is available at: DESCRIPTION http://dot.imgen.bcm.tmc.edu:9331/seq-search/Help/blastpat.html DESCRIPTION http://dot.imgen.bcm.tmc.edu:9331/seq-search/Help/fastpat.html AUTHOR Istvan Ladunga, Brent Wiese, and Randall F. Smith RT - ADDRESS Human Genome Center, Department of Molecular and Human Genetics ADDRESS and W.M. Keck Center for Computational Biology ADDRESS Baylor College of Medicine, Houston, TX 77030, USA ADDRESS tel: +1 713-798-8089 - fax: +1 713-798-5386 CONTACT {istvanl,brent,rsmith}@bcm.tmc.edu SITE WWW Server at URL http://gc.bcm.tmc.edu:8088/search-launcher/launcher.html OS - LANGUAGE - VOLUME - REQUIRES - AC BC00405 NAME MitoProt DOMAIN Protein sequence analysis DESCRIPTION It supplies a series of parameters that permit theoretical DESCRIPTION evaluation on mitochondrial targeting sequences, as well DESCRIPTION as two hydrophobicity related parameters that are important DESCRIPTION for predicting the putative importability of a protein into DESCRIPTION mitochondria. AUTHOR Manuel G. CLAROS RA Claros M.G.; RT "MitoProt, a Macintosh application for studying RT mitochondrial proteins."; RL Comput. Appl. Biosci. 11(4):441-447(1995). RX SeqAnalRef; CLAM9501. ADDRESS Biologia Molecular, Facultad Ciencias, ADDRESS E-29071 Malaga, Spain CONTACT claros@ccuma.uma.es SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/mac SITE-CONTACT nethelp@ebi.ac.uk SITE ftp anonymous ftp.bio.indiana.edu SITE Directory /molbio/mac SITE-CONTACT - SITE ftp anonymous ftp.ens.fr SITE Directory /pub/molbio SITE-CONTACT - OS MacOS systeme 6.02 or later LANGUAGE - VOLUME - REQUIRES - AC BC00414 NAME ProDom PROTEIN DOMAIN WWW SERVER DOMAIN WWW server DOMAIN Protein sequence analysis DOMAIN Alignment Search software DOMAIN Database and analysis DOMAIN Searching databases SERVER http://protein.toulouse.inra.fr/prodom.html DESCRIPTION ProDom is an automatically compiled database of protein domain families DESCRIPTION (Sonnhammer & Kahn, 1994, Protein Science, 3:482-492). It is useful for DESCRIPTION analyzing the domain organization of protein sequences. DESCRIPTION The ProDom WWW server allows one to: DESCRIPTION * Compare an amino acid or nucleic acid sequence to the domain family DESCRIPTION entries in the ProDom database. DESCRIPTION * Graphically and interactively analyze the ProDom domain arrangement DESCRIPTION of entire domain families. DESCRIPTION * Retrieve domain family entries. AUTHOR Jerome Gouzy, Elizabeth Ann Greene, Florence Corpet, AUTHOR Erik Sonnhammer, Daniel Kahn RA Sonnhammer E.L.L., Kahn D.; RT "Modular arrangement of proteins as inferred from analysis of homology."; RL Protein Sci. 3:482-492(1994). RX Medline; 94290324. RX SeqAnalRef; SONE9401. ADDRESS Laboratoire de Biologie Moleculaire ADDRESS des Relations Plantes-Microorganismes ADDRESS INRA-CNRS ADDRESS BP 27 ADDRESS Chemin de Borde Rouge ADDRESS 31326 Castanet Tolosan Cedex ADDRESS FRANCE CONTACT Daniel.Kahn@toulouse.inra.fr, Jerome.Gouzy@toulouse.inra.fr SITE WWW Server at URL http://protein.toulouse.inra.fr/prodom.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 BC00445 NAME ANTHEPROT Web page DOMAIN WWW server DOMAIN Protein sequence analysis DOMAIN Structure prediction DOMAIN Pattern Identification DOMAIN Alignment browser SERVER http://www.ibcp.fr/predict.html DESCRIPTION ANTHEPROT is a server that allows to make: DESCRIPTION * Secondary structure predictions: GOR, DPM, HOMOLOGUE, SOPMA, DESCRIPTION Phd DESCRIPTION * Multiple alignment : Clustalw (Higgins), Multalin (Corpet) DESCRIPTION * Search for biological sites using PROSITE DESCRIPTION * Search for homologous protein : Program FASTA (W. Pearson) AUTHOR G. Deleage, C. Geourjon, C. Blanchet RA Geourjon C., Deleage G.; RT "SOPM: a self-optimised meyhod for protein secondary RT struture prediction."; RL Protein Eng. 7:157-164(1994) RX Medline; 94224747. RX SeqAnalRef; GEOC9302. RA Geourjon C., Deleage G.; RT "SOPMA:significant improvements in protein secondary RT structure prediction by consensus prediction from RT multiple alignments."; RL Comput. Appl. Biosci. 11(6):681-684(1995). ADDRESS Institut de Biologie et Chimie des Proteines ADDRESS IBCP-CNRS UPR 412, Groupe de modelisation et RMN ADDRESS 7, Passage du Vercors ADDRESS 69 367 Lyon cedex 07, FRANCE CONTACT deleage@ibcp.fr, geourjon@ibcp.fr SITE WWW server at URL http://www.ibcp.fr/predict.html SITE-CONTACT geourjon@ibcp.fr or deleage@ibcp.fr OS - LANGUAGE - 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 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 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 BC00480 NAME ProMSED (Protein Multiple Sequence Editor) DOMAIN Protein sequence analysis DOMAIN Alignment Search software DOMAIN Alignment editing and display DESCRIPTION ProMSED, Windows 3.x/95 application for multiple protein DESCRIPTION sequences alignment, alignment analysis and editing. DESCRIPTION Reads several sequence formats, has main functions similar DESCRIPTION to MS Word text editor. Automatic alignment is based on DESCRIPTION ClustulV algorithm; manual alignment and visual analysis DESCRIPTION are facilitated by group and block operations and amino DESCRIPTION acid color coding reflecting their similarity in physico- DESCRIPTION chemical, mutational and other properties. AUTHOR Anatoly Frolov, Alexey Eroshkin RA Frolov A., Eroshkin A.; RT "ProMSED: Protein Multiple Sequence Editor for Windows 3.x/95."; RL In preparation ADDRESS A. Frolov, A. Eroshkin ADDRESS Mol. Biol. Res. Inst. ADDRESS SRC VB VECTOR ADDRESS Koltsovo, Novosibirsk region ADDRESS 633159 REussdia CONTACT eroshkin@vector.nsk.su SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/dos/promsed/ SITE-CONTACT nethelp@ebi.ac.uk SITE ftp anonymous ftp.bionet.nsc.ru SITE Directory /pub/biology/vector/promsed.dem/ OS Windows 3.x/95 LANGUAGE C++ VOLUME 600 Kb REQUIRES - COMMENTS ProMSED is distributed as self-extracted archiuve. Demo COMMENTS version has limits on length and number of sequences. AC BC00488 NAME GeneDoc DOMAIN Alignment editing and display DOMAIN Protein sequence analysis DOMAIN Phylogeny DESCRIPTION GeneDoc is a full featured Multiple Sequence Alignment Editor DESCRIPTION and Shading Utility. GeneDoc is also intended to help you bring DESCRIPTION your genetics research work to publication with lots of shading, DESCRIPTION page and font layout features. This is a utility that reads either DESCRIPTION .MSF Multiple Sequence alignment files or can Import Fasta Format DESCRIPTION files to be saved as a .MSF file project. DESCRIPTION GeneDoc is an alignment editor, that is it allows you to Edit the DESCRIPTION Alignment so that different residues from each sequence are lined DESCRIPTION up with each other. This is accomplished by moving the residues in DESCRIPTION one (or all but one) sequence relative to the other sequences by DESCRIPTION inserting or deleting gaps. GeneDoc also features the exclusive DESCRIPTION Grab and Drag mode, arranging residues like beads on a string. A DESCRIPTION residue editing mode is available to allow you to change the DESCRIPTION residues values themselves. Built in DayHoff and BlockSum scoring DESCRIPTION functions allow you to be sure your alignment changes are DESCRIPTION improving the score. Scores can be determined either by a Sum of DESCRIPTION Pairs method or with the Phylogenetic tree support. GUI DESCRIPTION implimentation makes it all so easy to use! DESCRIPTION GeneDoc also provides a comprehensive range of Display Shading DESCRIPTION Modes, functions and capabilities. Outlined below, these functions DESCRIPTION give flexible ways to look at the data and to show important DESCRIPTION concepts. Shading can even be done manually! DESCRIPTION GeneDoc provides output many different ways. You can print DESCRIPTION directly to the printer, export BitMaps, Text or MAC style Pict DESCRIPTION files. AUTHOR Karl Nicholas, Hugh Nicholas, PhD. RT - ADDRESS Karl Nicholas ADDRESS 566 Vallejo St. #34 ADDRESS San Francisco, CA, 94133 CONTACT ketchup@cris.com SITE WWW Server at URL http://www.cris.com/~ketchup/genedoc.shtml OS Win/3.1,Win/95,Win/NT LANGUAGE - 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 BC00498 NAME Map123d SERVER http://www-bio.lirmm.fr:8090/map123d.html DOMAIN WWW server DOMAIN Protein sequence analysis DOMAIN Protein structure analysis DOMAIN Structure prediction DOMAIN Alignment editing and display DOMAIN Molecular modelling and graphics SERVER http://www-bio.lirmm.fr:8090/map123d.html DESCRIPTION This server offers a set of tools for protein homology modelling. DESCRIPTION The "introduction" page provides a short overview on the DESCRIPTION problem of homology modelling and presents the tools DESCRIPTION available in this server: DESCRIPTION - Global multiple Alignment DESCRIPTION - Secondary structure prediction DESCRIPTION - Evaluation of a structural model AUTHOR H. Ripoche, J. Gracy, L. Chiche RT - ADDRESS LIRMM ADDRESS 161, Rue Ada ADDRESS 34392 MONTPELLIER Cedex 5 - France CONTACT hr@lirmm.fr SITE WWW Server at URL http://www-bio.lirmm.fr:8090/map123d.html OS - LANGUAGE - VOLUME - REQUIRES Java compatible browser (e.g. Netscape 2.0 or above) REQUIRES for some of the tools 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 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 BC00517 NAME ToPLign Toolbox for Protein aLignments DOMAIN Protein sequence analysis DOMAIN Alignment Search software DOMAIN Alignment editing and display DOMAIN Alignment browser DOMAIN WWW server SERVER http://cartan.gmd.de/ToPLign.html DESCRIPTION ToPLign implements standard pairwise and multiple alignment DESCRIPTION methods with flexible parameter handling. The analysis of DESCRIPTION alignments is supported by offering different DESCRIPTION visualisations of alignments. In addition, ToPLign DESCRIPTION includes innovative approaches to the parametric alignment DESCRIPTION problem and the threading problem. The development of the DESCRIPTION ToPLign package is part of the PROTAL project AUTHOR Heinz Mevissen, Ralf Thiele, Ralf Zimmer RA Mevissen H, Thiele, R., Zimmer, R., Lengauer, T.; RT "The ToPLign software environment - RT Toolbox for Protein ALignment"; RL Bioinformatics'94, IMB, Jena (1994). ADDRESS Heinz Mevissen ADDRESS Ralf Thiele ADDRESS Ralf Zimmer ADDRESS Thomas Lengauer ADDRESS German National Research Center for Information Technology ADDRESS Schloss Birlinghoven, D-53754 Sankt Augustin CONTACT Heinz-Theordor.Mevissen@gmd.de CONTACT Ralf.Thiele@gmd.de CONTACT Ralf.Zimmer@gmd.de SITE WWW Server at URL http://cartan.gmd.de/ToPLign.html OS - LANGUAGE - VOLUME - REQUIRES - 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 BC00530 NAME Band Leader DOMAIN Sequence tools DOMAIN Protein sequence analysis DOMAIN Genetic tools DESCRIPTION Band Leader is software for the PC Windows operating environment. DESCRIPTION It is very easy to use and requires only basic Windows skills. DESCRIPTION With Band Leader you process your gel images to extract data DESCRIPTION arranged in lanes or in spots. DESCRIPTION You may create graphs representing data along lanes which you may later DESCRIPTION process to extract band information. DESCRIPTION You may create Spot documents, representing single spots on the Gel DESCRIPTION image or use the Grid tool to extract a group of Spots. DESCRIPTION DESCRIPTION Band Leader data can be exported as flat text file or as Spreadsheet DESCRIPTION data. DESCRIPTION Band Leader is an MDI application, thus you may load more than DESCRIPTION one set of images to process at a time. AUTHOR Ma'ayan Aharoni - for Magnitec Ltd. RT - ADDRESS POB 39204, ADDRESS Tel-Aviv 61391, ADDRESS ISRAEL. CONTACT magnitec@world.std.com SITE WWW Server at URL http://ramat-negev.org.il/~amshav/magnitec.htm OS windows LANGUAGE Enghlish VOLUME 1 Meg REQUIRES Windows 3.0 and up AC BC00538 NAME DRAWHCA SERVER http://www.lmcp.jussieu.fr/~mornon DOMAIN WWW server DOMAIN Protein sequence analysis DOMAIN Protein structure analysis DESCRIPTION This WWW page enables you to draw an HCA (Hydrophobic Cluster DESCRIPTION Analysis)plot using the program drawhca. This server provides DESCRIPTION plots as colour or b&w PostScript files. AUTHOR Luc Canard, Alain Soyer RT - ADDRESS Jean-Paul Mornon ADDRESS Laboratoire de Mineralogie-Cristallographie - CNRS URA09 ADDRESS Universite Pierre et Marie Curie ADDRESS Tour 16, 2e etage, Boite 115 ADDRESS 4, place Jussieu ADDRESS F-75252 PARIS CEDEX 05 ADDRESS FRANCE CONTACT mornon@lmcp.jussieu.fr SITE WWW Server at URL http://www.lmcp.jussieu.fr/~mornon/ OS - LANGUAGE - VOLUME - REQUIRES - AC BC00543 NAME Visual BLAST (and Visual FASTA) DOMAIN Protein sequence analysis DOMAIN Alignment editing and display DESCRIPTION To facilitate and accelerate BLAST and FASTA output results, DESCRIPTION we present, for the first time, two easy-to-use programs DESCRIPTION designed for interactive analysis of full BLAST and FASTA DESCRIPTION output files containing protein sequence alignments. These DESCRIPTION programs, Visual BLAST and Visual FASTA, run under Microsoft DESCRIPTION Windows 95 or NT computers. They are based on the same DESCRIPTION intuitive graphical user interface (GUI) with extensive DESCRIPTION viewing, searching, editing, printing and multithreading DESCRIPTION capabilities. These programs improve the browsing of DESCRIPTION BLAST/FASTA results by offering a more convenient DESCRIPTION presentation of these results. They also implement on a DESCRIPTION computer several analytical tools which automate a manual DESCRIPTION methodology used for detailed analysis of BLAST and FASTA DESCRIPTION outputs. These tools include a pairwise sequence alignment DESCRIPTION viewer, a Hydrophobic Cluster Analysis plot alignment DESCRIPTION viewer and a tool displaying a graphical map of all DESCRIPTION database sequences aligned with the query sequence. DESCRIPTION In addition, Visual BLAST includes tools for multiple DESCRIPTION sequence alignment analysis (with an amino acid patterns DESCRIPTION search engine), and Visual FASTA provides a GUI to the DESCRIPTION FASTA program. AUTHOR Patrick DURAND, Luc Canard, Jean-Paul Mornon RA Durand P., Canard L., Mornon J.P. RT "Visual BLAST and Visual FASTA : graphic workbenches for RT interactive analysis of full BLAST and FASTA outputs RT under Microsoft Windows 95/NT"; RL Comput. Appl. Biosci. 13(4):407-413(1997). ADDRESS Patrick Durand ADDRESS Laboratoire de Mineralogie-Cristallographie/CNRS URA 09 ADDRESS Universite Pierre et Marie Curie ADDRESS Tour 16, 2e etage, Boite 115 ADDRESS 4, place Jussieu ADDRESS F-75252 PARIS CEDEX 05 ADDRESS FRANCE CONTACT durand@lmcp.jussieu.fr SITE WWW Server at URL http://www.lmcp.jussieu.fr/~durand/ OS Windows 95/NT LANGUAGE - VOLUME - REQUIRES - AC BC00547 NAME SAGA DOMAIN Protein sequence analysis DOMAIN Alignment Search software SERVER http://www.ebi.ac.uk/~cedric DESCRIPTION SAGA (Sequence Alignmnet by Genetic ALgorithm) DESCRIPTION is a genetic algorithm designed for aligning protein DESCRIPTION sequences using various objective functions AUTHOR Notredame and Higgins RA Notredame C., Higgins D.; RT "SAGA: Sequence Alignmnet by Genetic Algorithm."; RL Nucleic Acids Res. 24(8):1515-1524(1996). ADDRESS Cedric NOTREDAME ADDRESS EMBL Outstation - The EBI ADDRESS Wellcome Trust Genome Campus, ADDRESS Hinxton, Cambridge CB10 1SD U.K. CONTACT cedric.notredame@ebi.ac.uk SITE WWW Server at URL http://www.ebi.ac.uk/~cedric OS UNIX LANGUAGE C VOLUME - REQUIRES - AC BC00550 NAME GEANFAMMER DOMAIN Protein sequence analysis DESCRIPTION Protein sequence family generator at domain level. DESCRIPTION It uses search algorithms to search database(self self DESCRIPTION search) to cluster sequence domains with given score DESCRIPTION threshold to generate a list of clusters. DESCRIPTION It was used for genome sequence domain clustering. AUTHOR Sarah A. Teichmann, Jong H. Park RT CABIOS (Bioinformatics), in press (Dec. 1997) ADDRESS Sarah A. Teichmann ADDRESS Structural Studies, ADDRESS LMB, MRC Centre, Hills Road, Cambridge CB22QH, U.K. ADDRESS Jong Park ADDRESS Department of Genetics / HHMI ADDRESS Harvard Medical School ADDRESS Warren Alpert Building ADDRESS 200 Longwood Avenue ADDRESS Boston MA 02115, USA CONTACT sat@mrc-lmb.cam.ac.uk, CONTACT JPark@rascal.med.harvard.edu SITE WWW Server at URL http://www.mrc-lmb.cam.ac.uk/genomes/ OS LINUX,UNIX,NT,Windows,MAC LANGUAGE PERL VOLUME 2 mb for software, 1GB for running it REQUIRES Perl5, large disk space, AC BC00551 NAME The Gene Discovery Page DOMAIN WWW server DOMAIN Sequence tools DOMAIN Protein sequence analysis DOMAIN Genome Analysis SERVER http://www.geocities.com/CapeCanaveral/1915/gdp.html DESCRIPTION The purpose of this page is to serve as a "desktop" area, DESCRIPTION primarily for the bench scientist with little biocomputing DESCRIPTION background. It organizes existing search engines in a DESCRIPTION coherent, stepwise fashion providing one of the many DESCRIPTION strategies that may lead to gene discovery. AUTHOR Skoufos, Emmanouil RT - ADDRESS Center for Medical Informatics ADDRESS and Section of Neurobiology ADDRESS Yale University School of Medicine ADDRESS 333 Cedar Street ADDRESS New Haven, CT 06511 CONTACT emmanouil.skoufos@yale.edu SITE WWW Server at URL http://www.geocities.com/CapeCanaveral/1915/gdp.html SITE-CONTACT - OS - LANGUAGE - VOLUME - REQUIRES - Ac BC00557 NAME PESTFIND DOMAIN Protein sequence analysis DOMAIN Pattern Identification DESCRIPTION Finds PEST protein degradation signals in protein sequences. This version is DESCRIPTION a straight translation to ANSI C from the original BASICA DESCRIPTION version from Martin Rechsteiner's laboratory. AUTHOR David Mathog, Bob Stellwagen, Martin Rechsteiner RA - RT - RL J.Biol.Chem 266(17):11213-11220(1991). RL Science 234:364-368(1986). ADDRESS - CONTACT mathog@seqaxp.bio.caltech.edu SITE WWW Server at URL http://seqaxp.bio.caltech.edu/pub/SOFTWARE/ OS any LANGUAGE ANSI C VOLUME - REQUIRES ANSI C compiler, UNZIP program AC BC00564 NAME SEALS: A System for Easy Analysis of Lots of Sequences DOMAIN Sequence format conversion tools DOMAIN Sequence tools DOMAIN Protein sequence analysis DOMAIN Pattern Identification DOMAIN Genome Analysis DOMAIN Phylogeny DOMAIN Database and analysis DOMAIN Searching databases DESCRIPTION SEALS (A System for Easy Analysis of Lots of Sequences) is a DESCRIPTION free, public domain package for large-scale sequence analysis DESCRIPTION investigations. It is still under development, but already DESCRIPTION provides a number of very useful programs, including unique DESCRIPTION taxonomy-aware tools. AUTHOR Walker DR, Koonin EV RA Walker DR, Koonin EV; RT "SEALS: A System for Easy Analysis of Lots of Sequences"; RL ISMB 5:333-339(1997). ADDRESS D Roland Walker ADDRESS National Center for Biotechnology Information ADDRESS National Library of Medicine ADDRESS National Institutes of Health, Bldg. 38A ADDRESS Bethesda, MD 20894, USA ADDRESS Voice: +1 (301)435-5909 Fax: +1 (301)435-5909 ADDRESS email: walker@ncbi.nlm.nih.gov ADDRESS ADDRESS Eugene V. Koonin, PhD ADDRESS National Center for Biotechnology Information ADDRESS National Library of Medicine ADDRESS National Institutes of Health, Bldg. 38A ADDRESS Bethesda, MD 20894, USA ADDRESS Voice: +1(301)435-5913 Fax:+1 (301)480-9241 ADDRESS email: koonin@ncbi.nlm.nih.gov CONTACT walker@ncbi.nlm.nih.gov (Roland Walker) SITE WWW Server at URL http://www.ncbi.nlm.nih.gov/Walker/SEALS/index.html OS Unix LANGUAGE Perl VOLUME 150 MB REQUIRES a number of other programs and db detailed on the home page AC BC00565 NAME fetch.pl DOMAIN Sequence tools DOMAIN Protein sequence analysis DESCRIPTION fetch.pl is a simple swissprot sequence retrieval utility AUTHOR Alex Bateman, Jong Park, Bissan, Astrid Reinhardt, Sarah Teichmann RT - ADDRESS MRC Centre, Hills Road, Cambridge, CB2 2QH, UK CONTACT jhp20@cus.cam.ac.uk, xv00vx@salt2.med.harvard.edu SITE WWW Server at URL http://www.mrc-lmb.cam.ac.uk:80/genomes/jong/Fetch/ SITE WWW Server at URL http://arep.med.harvard.edu/labgc/jong/Fetch/ OS Linux, UNIX, NT, LANGUAGE Perl VOLUME - REQUIRES - AC BC00568 NAME JOY SERVER http://www-cryst.bioc.cam.ac.uk/cgi-bin/joy.cgi DOMAIN Protein sequence analysis DOMAIN Protein structure analysis DOMAIN Alignment editing and display DOMAIN WWW server DOMAIN Comparative analysis DESCRIPTION JOY is a program to annotate protein sequence alignments DESCRIPTION with three-dimensional (3D) structural features. It was DESCRIPTION developed to display 3D structural information in a sequence DESCRIPTION alignment and to help understand the conservation of amino DESCRIPTION acids in their specific local environments. The JOY DESCRIPTION representation now constitutes an essential part of the two DESCRIPTION databases of protein structure alignments: HOMSTRAD DESCRIPTION (http://www-cryst.bioc.cam.ac.uk/~homstrad) and CAMPASS DESCRIPTION (http://www-cryst.bioc.cam.ac.uk/~campass). It has also been DESCRIPTION successfully used for identifying distant evolutionary DESCRIPTION relationships. DESCRIPTION DESCRIPTION JOY takes an input alignment (or a single sequence) in a DESCRIPTION format similar to that of the NBRF/PIR format and produces a DESCRIPTION number of output files, including the annotated alignment in DESCRIPTION PostScript, LATEX and HTML. JOY requires a series of DESCRIPTION datafiles containing information about secondary structures, DESCRIPTION solvent accessibility and hydrogen bonding. These are DESCRIPTION produced automatically from a PDB file by supporting DESCRIPTION programs. AUTHOR Kenji Mizuguchi, Charlotte M. Deane, Tom L. Blundell, AUTHOR Mark S. Johnson, John P. Overington RA Mizuguchi K., Deane C.M., Johnson M.S., Blundell T.L., Overington J.P.; RT "JOY: protein sequence-structure representation and analysis."; RL Bioinformatics 14:617-623(1998). ADDRESS Department of Biochemistry ADDRESS University of Cambridge ADDRESS 80 Tennis Court Road ADDRESS Cambridge CB2 1GA ADDRESS UK CONTACT kenji@cryst.bioc.cam.ac.uk SITE WWW Server at URL http://www-cryst.bioc.cam.ac.uk/cgi-bin/joy.cgi OS UNIX LANGUAGE Fortran, C, Perl VOLUME - REQUIRES - COMMENTS Currently only executable files for IRIX5.3 or highter are COMMENTS available, but distribution of the source code to academic COMMENTS users will follow. AC BC00574 NAME nrdb90 DOMAIN Protein sequence analysis DOMAIN Searching databases DESCRIPTION To maximize the chances of biological DESCRIPTION discovery, homology searching must use an up-to-date DESCRIPTION combination of multiple sequence databases. nrdb90 clusters DESCRIPTION the sequence database yielding a representative subset that DESCRIPTION is faster to search and improves the consistency of DESCRIPTION sequence annotation. The generation of a representative set DESCRIPTION is effectively an all-against-all comparison problem. DESCRIPTION nrdb90 uses a fast and complete lookup algorithm for the DESCRIPTION removal of fragments and close similarities. Search space DESCRIPTION is pruned using deca- and pentapeptide composition filters DESCRIPTION that leave a minimal fraction of pairs for which sequence DESCRIPTION identity is determined by explicit alignment. The union of DESCRIPTION the Swissprot, Swissnew, Trembl, Tremblnew, Genbank, PIR, DESCRIPTION Wormpep and PDB databases, containing 260,000 non-duplicate DESCRIPTION sequences, was processed in 2 days CPU time and yielded a DESCRIPTION representative set at 90 % sequence identity with a size DESCRIPTION reduction of 46 %. AUTHOR L. Holm & C. Sander RA Holm, L. and Sander, C.; RT "Removing near-neighbour redundancy from large protein sequence RT collections."; RL Bioinformatics 14:423-429(1998). ADDRESS L. Holm ADDRESS EMBL-EBI ADDRESS Wellcome Trust Genome Campus, Hinxton, ADDRESS Cambridge CB10 1SD ADDRESS U.K. CONTACT holm@embl-ebi.ac.uk SITE WWW Server at URL http://www.ebi.ac.uk/~holm/nrdb90 OS - LANGUAGE Perl VOLUME - REQUIRES - AC BC00579 NAME Pyramids DOMAIN Protein sequence analysis DOMAIN Genome Analysis DOMAIN Phylogeny DESCRIPTION PYRAMIDS is a set of programs to create and draw a DESCRIPTION pyramidale representation of a set of sequences (given DESCRIPTION their relative distance). DESCRIPTION a pyramidal representation is a planar graph (close DESCRIPTION to upgma-like trees). DESCRIPTION DESCRIPTION one of the key feature of a pyramidal representation, DESCRIPTION is that a sequence can belong to two cluster. AUTHOR Jean-Christophe Aude. RA Aude J.C. , Diaz-Lazcoz Y. , Codani J.J. and Risler J.L.; RT "Application of the pyramidal clustering method to RT biological objects"; RL Computer & Chemistry, special issue - [accepted] ADDRESS Universite Versailles/Saint-Quentin - CGM/CNRS, FRANCE CONTACT jean-christophe.aude@inria.fr SITE WWW Server at URL http://genome.genetique.uvsq.fr/Pyramids OS SunOS, Solaris, Linux, Digital Unix, SGI Irix LANGUAGE - VOLUME 150ko REQUIRES transfig for postscript conversion (optional) COMMENTS A java application that allow you to display the pyramid COMMENTS is also available from the web site. AC BC00588 NAME DAMBE (Data analysis in molecular biology and evolution) DOMAIN Sequence format conversion tools DOMAIN Sequence display DOMAIN Sequence analysis DOMAIN Sequence tools DOMAIN Protein sequence analysis DOMAIN Protein structure analysis DOMAIN Alignment editing and display DOMAIN Alignment browser DOMAIN Genetic tools DOMAIN Molecular Evolution DOMAIN Phylogeny DOMAIN Database and analysis DOMAIN Searching databases DOMAIN General tools DOMAIN Statistical significance DOMAIN Comparative analysis DESCRIPTION DAMBE (Data Analysis in Molecular Biology DESCRIPTION and Evolution) is an integrated software package for DESCRIPTION converting, manipulating, statistically and graphically DESCRIPTION describing and analyzing molecular sequence data, with a DESCRIPTION user-friendly Windows 95 interface. AUTHOR Xuhua Xia RT - ADDRESS Department of Ecology & Biodiversity, ADDRESS University of Hong Kong, Hong Kong CONTACT xxia@hkusua.hku.hk SITE WWW Server at URL http://web.hku.hk/~xxia/software/software.htm OS Windows 95 LANGUAGE - VOLUME 10 MB REQUIRES Windows 95 AC BC00592 NAME nrdb90 DOMAIN Protein sequence analysis DOMAIN Searching databases DESCRIPTION To maximize the chances of biological discovery, homology DESCRIPTION searching must use an up-to-date combination of multiple DESCRIPTION sequence databases. nrdb90 clusters the sequence database DESCRIPTION yielding a representative subset that is faster to search DESCRIPTION and improves the consistency of sequence annotation. The DESCRIPTION generation of a representative set is effectively an DESCRIPTION all-against-all comparison problem. nrdb90 uses a fast and DESCRIPTION complete lookup algorithm for the removal of fragments and DESCRIPTION close similarities. Search space is pruned using deca- and DESCRIPTION pentapeptide composition filters that leave a minimal DESCRIPTION fraction of pairs for which sequence identity is determined DESCRIPTION by explicit alignment. The union of the Swissprot, DESCRIPTION Swissnew, Trembl, Tremblnew, Genbank, PIR, Wormpep and PDB DESCRIPTION databases, containing 260,000 non-duplicate sequences, was DESCRIPTION processed in 2 days CPU time and yielded a representative DESCRIPTION set at 90 % sequence identity with a size reduction of 46 DESCRIPTION %. AUTHOR L. Holm & C. Sander RA Holm L. and Sander C. RT "Removing near-neighbour redundancy from large protein RT sequence collections."; RL Bioinformatics 14, 423-429 (1998). ADDRESS L. Holm ADDRESS EMBL-EBI ADDRESS Cambridge CB10 1SD ADDRESS U.K. CONTACT holm@embl-ebi.ac.uk SITE WWW Server at URL http://www.ebi.ac.uk/~holm/nrdb90 OS - LANGUAGE Perl VOLUME - REQUIRES - AC BC00594 NAME Protein Adviser for Windows DOMAIN Sequence format conversion tools DOMAIN Sequence display DOMAIN Protein sequence analysis DOMAIN Protein structure analysis DOMAIN Molecular modelling and graphics DOMAIN General tools DOMAIN Chemistry DOMAIN Image analysis DOMAIN Comparative analysis DOMAIN Protein 3D visualisation, editing and analysis (QSAR) DESCRIPTION FQS Protein Adviser displays and analyses 3D structures of DESCRIPTION biological molecules such as proteins or nucleic acids. DESCRIPTION Protein Adviser is a powerful tool for visual and numerical DESCRIPTION investigation of protein molecules and their 3D structures. DESCRIPTION The new implementation for Windows 95/98 and NT uses the DESCRIPTION innovative Microsoft technology for rendering molecular DESCRIPTION graphics known as Direct3D. Using Direct 3D technology FQS DESCRIPTION created the fastest biomolecular viewer available on PC DESCRIPTION platform. DESCRIPTION Versatile features to support protein analysis: DESCRIPTION - sequence based 3D analysis DESCRIPTION - Three level selections: atoms, residues, molecules DESCRIPTION - Display/Hide hydrogen's DESCRIPTION - Display/Hide side chain DESCRIPTION - Hydrogen generation DESCRIPTION - Measure atom-atom distances DESCRIPTION - Compare 3D structures DESCRIPTION - Compare aminoacid sequences DESCRIPTION - Analyze Ramachandran plots DESCRIPTION - Mutate and change side chain conformations DESCRIPTION - Build proteins, change torsional angles DESCRIPTION - Copy and paste molecules between the windows DESCRIPTION - Rotate and move selected molecules DESCRIPTION Windows specific features DESCRIPTION Protein Adviser can open as many documents DESCRIPTION as you wish and analyse them within one program session, DESCRIPTION Protein Adviser implements full ActiveX/OLE2 functionality. DESCRIPTION Its objects (molecules) may be placed on your WEB page and DESCRIPTION visualized by your colleagues everywhere through the DESCRIPTION internet. DESCRIPTION Plotting hydrophobicity and other properties DESCRIPTION Protein Adviser for Windows can plot DESCRIPTION different named properties. The program comes with 3 DESCRIPTION different scales of hydrophobicty, including Kyte&Doolittle DESCRIPTION scale. The program includes also 6 other predefined QSAR DESCRIPTION methods. DESCRIPTION Plotting Ramachandran diagrams DESCRIPTION Ramachandran plots show two-dimensional DESCRIPTION histograms of the values of conformational angles phi and DESCRIPTION psi. These histograms are superimposed on the areas of DESCRIPTION allowed and forbidden conformational angles pair values. DESCRIPTION Aminoacids DESCRIPTION Protein Adviser displays sequences of DESCRIPTION aminoacids as 3-letter codes, 1-letter codes or secondary DESCRIPTION structure symbols DESCRIPTION Protein's 3D structure comparison DESCRIPTION Protein Adviser for Windows allows for DESCRIPTION protein structure comparison command. The program DESCRIPTION superimposes the protein's 3D structures based on C(alpha) DESCRIPTION atoms coordinates and RMSD analysis. AUTHOR FQS Ltd. (Fujitsu Kyushu System Engineering Ltd.) RT - ADDRESS FQS Poland Sp. z o.o. ADDRESS Palac Pugetow ADDRESS ul. Starowislna 13-15 ADDRESS 31-038 Krakow ADDRESS Poland ADDRESS Tel. (+48 12) 4294345 ADDRESS Fax. (+48 12) 4296124 CONTACT info@fqspl.com.pl SITE WWW Server at URL http://www.fqspl.com.pl/protein OS Windows 95/98/NT, Macintosh LANGUAGE English, Japanese VOLUME 10 MB REQUIRES PC Pentium 166, 16MB RAM, Microsoft DirectX COMMENTS Commercial software. COMMENTS Price: COMMENTS 800 USD - commercial license & COMMENTS 400 USD - academic licence 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 BC00600 NAME Jpred - consensus secondary structure prediction server DOMAIN Protein sequence analysis DOMAIN Protein structure analysis DOMAIN Structure prediction DOMAIN JAVA DOMAIN WWW server SERVER http://barton.ebi.ac.uk/servers/jpred.html DESCRIPTION Jpred is a internet web server that takes DESCRIPTION either a protein sequence or a mulitple alignment of DESCRIPTION protein sequences, and predicts secondary structure. It DESCRIPTION works by combining a number of modern, high quality DESCRIPTION prediction methods to form a consensus. DESCRIPTION DESCRIPTION Jpred runs DSC, PHD, PREDATOR and NNSSP to build it's consensus DESCRIPTION prediction, but predictions from older algorithms Mulpred and DESCRIPTION Zpred are also included in the final output. DESCRIPTION DESCRIPTION The consensus method has been shown, to be DESCRIPTION on average more accurate than any of the component methods, DESCRIPTION by ca. 1%. However the strength of this server lies in the DESCRIPTION fact that it leaves the final decision to the user who can DESCRIPTION use the supplied coloured HTML and Java viewer to decide DESCRIPTION where the best or most sensible consensus may be. AUTHOR Cuff J. A., Clamp M. E., Siddiqui A. S., Finlay M., Barton G. J. RA Cuff J. A. and Barton G. J.; RT "Evaluation and improvement of multiple sequence methods RT for protein secondary structure prediction."; RL PROTEINS: Structure, Function and Genetics. 34:508-519 (1999). RA Cuff, J. A., Clamp, M. E., Siddiqui, A. S., Finlay, M. RA and Barton, G. J. RT "Jpred: a consensus secondary structure prediction server."; RL Bioinformatics 14:892-893 (1998). ADDRESS EMBL-European BioInformatics Institute, ADDRESS Wellcome Trust Genome Campus, Hinxton Cambs. ADDRESS CB10 1SD, UK CONTACT geoff@ebi.ac.uk SITE WWW Server at URL http://barton.ebi.ac.uk/servers/jpred.html OS - LANGUAGE - VOLUME - REQUIRES Netscape/IE > 4, with JAVA 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 AC BC00602 NAME ProtEST Protein Multiple Sequence Alignments from ESTs DOMAIN Protein sequence analysis DOMAIN WWW server SERVER http://barton.ebi.ac.uk/servers/protest.html DESCRIPTION ProtEST Protein Multiple Sequence Alignments from ESTs DESCRIPTION ProtEST allows you to search an EST DESCRIPTION (expressed sequence tag) database with a protein. The DESCRIPTION significant hits are automatically checked and filtered DESCRIPTION before being aligned. DESCRIPTION ProtEST was written to solve the problem where you need a DESCRIPTION protein multiple sequence alignment e.g. for secondary DESCRIPTION structure prediction, and yet there are no sequences to be DESCRIPTION found in the current protein sequence database. AUTHOR Cuff J. A., E. Birney., M. E. Clamp, Barton G. J. RA Cuff J. A., E. Birney., M. E. Clamp, Barton G. J.; RT "ProtEST: Protein multiple sequence alignments from ESTs."; RL Bioinformatics: submited (1999) ADDRESS EMBL-European BioInformatics Institute, ADDRESS Wellcome Trust Genome Campus, Hinxton Cambs. ADDRESS CB10 1SD - UK CONTACT geoff@ebi.ac.uk SITE WWW Server at URL http://barton.ebi.ac.uk/servers/protest.html OS - LANGUAGE - VOLUME - REQUIRES Netscape/IE > 4, with JAVA