Catalogue of Molecular Biology Programs Release 6.1 23 Jul 1999 All thanks are in the file biocatal.thanks. ===================================================================== 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 BC00207 NAME ACCESS DOMAIN Searching databases DOMAIN GCG tools DESCRIPTION Locate entry in Protein or Nucleic sequence DESCRIPTION Databases by means of the Accession Number or DESCRIPTION the Sequence Identification. Answers the DESCRIPTION question: Where is and how can I retrieve the DESCRIPTION sequence M10112 ? AUTHOR Prilusky J. RT - ADDRESS Weizmann Institute of science ADDRESS P.O.B. 26, Rehovot 76100, Israel CONTACT lsprilus@weizmann.weizmann.ac.il 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 Vax/Vms Unix LANGUAGE Pascal VOLUME - REQUIRES requires GCG 7.0 AC BC00208 NAME CLEVER DOMAIN Searching databases DESCRIPTION COmmand Line Entrez VERsion DESCRIPTION clever is a character based version of NCBI's Entrez program. DESCRIPTION It is an interactive tool that allows easy browsing of the DESCRIPTION Entrez database. AUTHOR Pierre Rioux, William A. Gilbert, Tim Littlejohn RT - ADDRESS - CONTACT For more information about the clever project, send email to CONTACT the Informatics Division of the Organelle Genome Megasequencing CONTACT Unit at the Universite de Montreal: ogmp@bch.umontreal.ca SITE ftp anonymous megasun.bch.umontreal.ca SITE Directory /pub/clever SITE-CONTACT - OS clever will run on any hardware/operating system combination OS that are supported by the NCBI toolkit LANGUAGE - VOLUME - AC BC00209 NAME ENTREZ DOMAIN Searching databases DESCRIPTION Entrez is a molecular sequence retrieval DESCRIPTION system developed at the National Center for DESCRIPTION Biotechnology Information (NCBI) DESCRIPTION Entrez provides an integrated approach for DESCRIPTION gaining access to nucleotide and protein DESCRIPTION sequence information, to the MEDLINE citations DESCRIPTION in which the sequences were published, and to DESCRIPTION a sequence-associated subset of MEDLINE. The DESCRIPTION sequence records are derived from a variety of DESCRIPTION database sources, including GenBank, EMBL, DESCRIPTION DDBJ, PIR, SWISS-PROT, PRF, and PDB. With DESCRIPTION Entrez and a personal computer, you can rapidly DESCRIPTION search several hundred megabytes of sequence DESCRIPTION and literature data using techniques that are DESCRIPTION fast and intuitive. The retrieval software and DESCRIPTION associated databases are distributed on CD- DESCRIPTION ROMs, but may be mounted on a file server and DESCRIPTION installed on multiple computers on a local DESCRIPTION network if desired. DESCRIPTION The /entrez/current directory of the NCBI DESCRIPTION anonymous ftp server is used for updates to DESCRIPTION the Entrez executables for a given release of DESCRIPTION the Entrez: Sequences and Entrez: References DESCRIPTION CD-ROMs. The Entrez application requires that DESCRIPTION you obtain the NCBI Entrez CD-ROMs.To request DESCRIPTION subscription information on Entrez, please DESCRIPTION send an email message to info@ncbi.nlm.nih.gov. DESCRIPTION Include your full postal address and your phone DESCRIPTION and fax numbers. AUTHOR - RT - ADDRESS - CONTACT - SITE ftp anonymous ncbi.nlm.nih.gov SITE Directory /entrez SITE-CONTACT info@ncbi.nlm.nih.gov OS SUN SPARCstation, SGI Iris workstation, OS Macintosh, or IBM-PC with Microsoft OS Windows platforms. LANGUAGE C VOLUME - AC BC00210 NAME OVERSEER DOMAIN Searching databases DESCRIPTION A package for searching nucleic acid sequence data DESCRIPTION bases AUTHOR Sibbald P. RA Sibbald P.R., Sommerfeldt H., Argos P.; RT "Overseer: a nucleotide sequence searching tool."; RL Comput. Appl. Biosci. 8:45-48(1992). RX Medline; 92233298. RX SeqAnalRef; SIBP9201. ADDRESS EMBL, Heidelberg, Germany CONTACT sibbald@embl-heidelberg.de SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/vax VAX software are stored as SITE uuencoded (.UUE) files. 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 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 Unix LANGUAGE Pascal VOLUME - AC BC00211 NAME PSQ DOMAIN Searching databases DESCRIPTION Protein Sequence Database Retrieval System AUTHOR - RT - ADDRESS - CONTACT Kathryn Sidman, Protein Identification CONTACT Resource National Biomedical Research CONTACT Foundation, pirmail@gunbrf.bitnet SITE - SITE-CONTACT - OS VAX/VMS LANGUAGE - VOLUME - AC BC00213 NAME SEQF DOMAIN Searching databases DESCRIPTION Package of programs for searching genetic DESCRIPTION sequence libraries. AUTHOR Davison D. and Kanehisa M. RT - ADDRESS - CONTACT Dan Davison: dbd@theory.bchs.uh.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-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 FORTRAN VOLUME - AC BC00214 NAME SRS DOMAIN Searching databases DESCRIPTION SRS is a Sequence Retrieval System DESCRIPTION information indexing and retrieval system designed for libraries DESCRIPTION with a flat file format. SRS supports the data structure of these DESCRIPTION libraries by providing special indices for, eg, implementing DESCRIPTION lists of subentities (e.g. feature tables). Indexing of DESCRIPTION cross-references allows a complete network of libraries to be DESCRIPTION built. In the network an entry from one library can be linked to DESCRIPTION every other library either directly or with a succession of DESCRIPTION single links between neighboring, cross-referenced, libraries. DESCRIPTION A language ODD (Object, Design and Definition) has been designed DESCRIPTION and developed to structure and define the data to cope with DESCRIPTION different library formats subject to continuous change. AUTHOR Etzold T. RA Etzold T., Argos P.; RT "SRS - an indexing and retrieval tool for flat file data libraries."; RL Comput. Appl. Biosci. 9:49-57(1993). RX Medline; 93169498. RX SeqAnalRef; ETZT9301. RA Etzold T., Argos P.; RT "Transforming a set of biological flat RT file libraries to a fast access network."; RL Comput. Appl. Biosci. 9:59-64(1993). RX Medline; 93169499. RX SeqAnalRef; ETZT9302. ADDRESS EMBL, Heidelberg, Germany. CONTACT Thure Etzold etzold@embl-heidelberg.de CONTACT Rodrigo Lopez rodrigol@biotek.uio.no CONTACT Reinhard Doelz doelz@urz.unibas.ch SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/vax/srs files: srs3_1.bck SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/unix/srs files: srs3_1.tar.Z SITE gopher Host: felix.embl-heidelberg.de Port: 70 SITE URL gopher://felix.embl-heidelberg.de:70/11/EMBnet BioInformation Resource EMBL/Software SITE WWW Server at URL http://www.ebi.ac.uk/srs/srsc SITE-CONTACT nethelp@ebi.ac.uk SITE ftp anonymous biomed.uio.no SITE Directory / files: srs3_1.bck SITE Additional files: fixrec.c and fixrec.com SITE gopher to Norwegian EMBnet node Host: biomaster.uio.no Port: 70 SITE URL gopher://biomaster.uio.no:70/11/About the NorwegianEMBnet node/SRS31 SITE is here/srs3_1.tar.Z OS VAX/VMS & OpenVMS , Unix LANGUAGE - VOLUME - AC BC00215 NAME STATSEARCH DOMAIN Searching databases DESCRIPTION Database searching taking into account the DESCRIPTION statistical significance of any similarities DESCRIPTION found AUTHOR R. Mott. RA Mott R.F., Kirkwood T.B.L.; RT "STATSEARCH: a GCG-compatible program for assessing statistical RT significance during DNA and protein databank searches."; RL Comput. Appl. Biosci. 6:293-295(1990). RX Medline; 91003525. RX SeqAnalRef; MOTR9003. ADDRESS National Institutes for Medical Research MRC CONTACT r-mott@nimr.mrd.ac.uk SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/vax (statsrch) VAX software are SITE stored as 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 Unix VAX/VMS LANGUAGE FORTRAN VOLUME - AC BC00216 NAME XYLEM DOMAIN Searching databases DESCRIPTION XYLEM is a package of tools designed to exploit DESCRIPTION the Unix environment to enable the user to DESCRIPTION identify, extract and manipulate data from major DESCRIPTION databases such as GenBank, EMBL and PIR. DESCRIPTION Fundamental to the power of these programs is DESCRIPTION the ability to perform operations on groups DESCRIPTION of sequences, represented by names or accession DESCRIPTION numbers which function as virtual database DESCRIPTION subsets. AUTHOR Brian Fristensky RA Fristensky, B.; RT "Feature expressions: creating RT and manipulating sequence datasets."; RT Nucleic Acids Res. 21:5997-6003(1993). RX Medline; 94119702. RX SeqAnalRef; FRIB9301. ADDRESS Dept. of Plant Science, University of Manitoba ADDRESS Winnipeg, MB R3T 2N2 CANADA ADDRESS tel: (1 204) 474-6085 Fax:(1 204) 261-5732 CONTACT Brian Fristensky frist@cc.umanitoba.ca SITE ftp anonymous ftp.cc.umanitoba.ca SITE Directory /psgendb SITE-CONTACT Brian Fristensky: frist@cc.umanitoba.ca SITE WWW Server at URL http://home.cc.umanitoba.ca/~psgendb/XYLEM.html OS Sun-3 and Sun-4, Unix LANGUAGE Pascal, C, csh. VOLUME - COMMENTS XYLEM is compatible with the Fristensky COMMENTS Sequence Analysis Package, and the Pearson COMMENTS FASTA programs, and can be usedfrom within the COMMENTS Genetic Data Environment (GDE) of Steven COMMENTS Smith. 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 BC00309 NAME OMIM DOMAIN WWW Server DOMAIN Searching databases DESCRIPTION The OMIM(TM)- Online Mendelian Inheritance in Man database, is a DESCRIPTION catalog of human genes and genetic disorders authored and edited DESCRIPTION by Dr. Victor A. McKusick and colleagues at Johns Hopkins and DESCRIPTION elsewhere, and developed for the World Wide Web by NCBI, the DESCRIPTION National Center for Biotechnology Information. The database DESCRIPTION contains textual information, pictures, and reference DESCRIPTION information. It also contains copious links to NCBI's Entrez DESCRIPTION database of MEDLINE articles and sequence information. AUTHOR OMIM is a trademark of the Johns Hopkins University. RT - ADDRESS National Center for Biotechnology Information ADDRESS National Library of Medicine ADDRESS Building 38A, Room 8N805 ADDRESS Bethesda, MD 20894, USA CONTACT info@ncbi.nlm.nih.gov SITE WWW server at URL http://www3.ncbi.nlm.nih.gov/omim/ SITE-CONTACT info@ncbi.nlm.nih.gov SITE ftp anonymous ncbi.nlm.nih.gov SITE Directory /repository/OMIM SITE-CONTACT info@ncbi.nlm.nih.gov OS - LANGUAGE Text file in the FTP site VOLUME - AC BC00354 NAME PATMAT DOMAIN Pattern Identification DOMAIN Searching databases DESCRIPTION General database searching tool with a simple and clear user DESCRIPTION interface. Can searches PROSITE.DAT as a pattern database. DESCRIPTION Searches other databases with patterns as probes. AUTHOR James C. Wallace RA Wallace J.C., Henikoff S.; RT "PATMAT: a searching and extraction program for sequence, RT pattern and block queries and databases."; RL Comput. Appl. Biosci. 8:249-254(1992). RX Medline; 92339038. RX SeqAnalRef; WALJ9201. ADDRESS Fred Hutchinson Cancer Research Center ADDRESS 1124 Columbia Street, Seattle, WA 98104, USA ADDRESS Tel: +1-206-6674501 CONTACT root@fred.fhcrc.org SITE ftp anonymous ncbi.nlm.nih.gov SITE Directory /repository/blocks/patmat.dos (for dos version) SITE-CONTACT - OS DOS 3.1 and higher, Unix LANGUAGE - VOLUME - REQUIRES - AC BC00361 NAME QUELSITE DOMAIN Searching databases DESCRIPTION QUELSITE is a program which is integrated in the BISANCE DESCRIPTION structure (national server in France). It permits to query all DESCRIPTION items of the PROSITE database as keywords, patterns, access or DESCRIPTION documentation numbers. AUTHOR C. Valencien RA Dessen P., Fondrat C., Valencien C., Mugnier C.; RT "BISANCE: A French service for access to biomolecular sequence RT databases."; RL Comput. Appl. Biosci. 6:355-356(1990). RX Medline; 91077760. RX SeqAnalRef; DESP9001. ADDRESS BISANCE - CITI2, 45 rue des Saints-Peres ADDRESS 75270 Paris Cedex 06, France ADDRESS Tel: +33-1-42962489 CONTACT bisance@citi2.fr SITE - SITE-CONTACT - OS Vax/VMS LANGUAGE FORTRAN VOLUME - REQUIRES - AC BC00365 NAME EMBL-Search DOMAIN Searching databases DESCRIPTION EMBL-Search is a free database query and retrieval program for DESCRIPTION the Apple MacIntosh for use with the EMBL Sequence Databases DESCRIPTION CD-ROM. Allows text queries of the PROSITE protein pattern DESCRIPTION database, in addition to the EMBL nucleotide and SWISS-PROT DESCRIPTION protein sequence databases. Cross-references between EMBL, DESCRIPTION SWISS-PROT, PROSITE (data), and PROSITE (doc) can be used to DESCRIPTION navigate easily between these databases. AUTHOR Rainer Fuchs RA Fuchs R., Stoehr P.; RT "EMBL-Search - A CD-ROM based database query system."; RL Comput. Appl. Biosci. 9:71-77(1993). RX Medline; 93169501. RX SeqAnalRef; FUCR9301. ADDRESS EBI - EMBL outstation, ADDRESS Hinxton Hall, Hinxton, Cambridge CB10 1RQ, UK CONTACT stoehr@ebi.ac.uk SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/mac SITE-CONTACT nethelp@ebi.ac.uk SITE WWW Server at URL http://www.ebi.ac.uk OS MacOS (systeme 7) LANGUAGE - VOLUME - REQUIRES EMBL Sequence database CD-ROM COMMENTS This program is used with the EMBL Sequence database CD-ROM COMMENTS See entry BC00453 for the MS-Windows version. AC BC00366 NAME GeneMan DOMAIN Searching databases DESCRIPTION GENEMAN is the only desktop sequence search DESCRIPTION tool that supports Boolean searches based on both text DESCRIPTION and sequence information. The major sequence DESCRIPTION databases are stored conveniently on CD-ROM, precluding DESCRIPTION problems with Internet bottlenecks. GENEMAN sorts the data DESCRIPTION retrieved, generates statistical summaries of search results, DESCRIPTION and generates data subsets. 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 BC00377 NAME Seq-Eudora-Blast DOMAIN Searching databases DESCRIPTION 2 sets of Macintosh AppleScript applications that DESCRIPTION automate your BLAST searches. One set, the "droplets", take DESCRIPTION Drag-and-Dropped text files containing DNA or protein sequence, DESCRIPTION extract the sequence from them, and send them to the BLAST DESCRIPTION server at ncbi.nlm.nih.gov using the mail application Eudora. DESCRIPTION The second set takes a DNA or protein sequence copied to the DESCRIPTION Clipboard and sends it to the BLAST server using Eudora. The DESCRIPTION mail messages specify BLAST parameters which are taken DESCRIPTION automatically from an accompanying text file called "BLAST DESCRIPTION parameters". AUTHOR Osborne, Brian I. RT - ADDRESS Plant Gene Expression Center,800 Buchanan St.,Albany CA 94710 USA CONTACT bosborne@nature.berkeley.edu SITE ftp anonymous ftp.bio.indiana.edu SITE Directory /molbio/mac SITE-CONTACT - OS Macintosh LANGUAGE English VOLUME - REQUIRES AppleScript,Eudora 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 BC00412 NAME WPDB DOMAIN Searching databases DESCRIPTION WPDB (the Protein Data Bank through DESCRIPTION Microsoft Windows) is a PC based software package DESCRIPTION comprising a compressed version of all or parts of the DESCRIPTION PDB and a set of tools to query features of a single DESCRIPTION structure or perform a comparative analysis on DESCRIPTION multiple structures with emphasis on sequence DESCRIPTION alignment and structure superposition. AUTHOR Ilya N. Shindyalov, Philip E. Bourne RT - RL J. App. Cryst. 28(6):847-852(1995). ADDRESS San Diego Supercomputer Center ADDRESS PO Box 85608 ADDRESS San Diego CA 92186-9784, USA ADDRESS Tel: +1 (619) 534-8301 - Fax: +1 (619) 534-5113 CONTACT bourne@sdsc.edu SITE WWW Server at URL http://www.sdsc.edu/CCMS/Packages/wpdb.html SITE ftp anonymous at ftp.sdsc.edu SITE Directory /pub/sdsc/biology/WPDB/ OS PC with MS-Windows LANGUAGE C++ VOLUME Software apprx. 3MB full compressed PDB (3,500 structures 70MB) COMMENTS To subscribe to the mailing list: Send the message COMMENTS subscribe wpdb to majordomo@sdsc.edu REQUIRES 486/33 with Microsoft Windows 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 BC00431 NAME RNCBI2 DOMAIN Searching databases DESCRIPTION Graphical frontend program for the retrieval of biological DESCRIPTION database entries from e-mail servers at the NLM/NIH, EMBL, and DESCRIPTION other sites including simple blast analysis requests of DNA and DESCRIPTION AA sequences at the blast server of NCBI/NIH. AUTHOR Sebastian Bunka RT - ADDRESS Institute of Medical Chemistry, University ADDRESS of Veterinary Medicine, Linke Bahngasse 11, ADDRESS A-1030 Vienna, AUSTRIA. ADDRESS Tel: (+43)-1-711 55 306, Fax: (+43)-1-713 68 95 CONTACT Sebastian.Bunka@vu-wien.ac.at SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/unix/rncbi SITE-CONTACT nethelp@ebi.ac.uk OS Unix LANGUAGE tcl/tk VOLUME - REQUIRES X11R5/6, tcl 7.3, and tk 3.6 COMMENTS Source code of the interpreted language tcl with tk extensions. COMMENTS Complete package is free software (C) by Sebastian Bunka under COMMENTS the terms of the Gnu General Public License. AC BC00434 NAME GDB Human Genome Data Base DOMAIN Genome Mapping Databases DOMAIN Database and analysis DOMAIN Searching databases DOMAIN WWW server SERVER http://gdbwww.gdb.org/ DESCRIPTION The GDB Human Genome Data Base is a public repository of genetic DESCRIPTION and physical maps of the human genome. It contains information DESCRIPTION about genomic regions (genes and other landmarks), mapping reagents, DESCRIPTION maps, genetic polymorphism, literature references, and contact DESCRIPTION information. GDB is an international collaboration DESCRIPTION hosted at Johns Hopkins University. AUTHOR Kenneth Fasman RA Fasman, K.H., Letovsky, S.I., Cottingham, R.W., Kingsbury, D.T.; RL Nucleic Acids Res. in press (1996). RA Fasman, K.H., Cuticchia, A.J., Kingsbury, D.T.; RT "The GDB human genome data base anno 1994."; RL Nucleic Acids Res. 22:3462-3469 (1994). RX Medline; 95023073. RX SeqAnalRef; FASK9401. ADDRESS Genome Data Base ADDRESS 2024 E. Monument Street, Suite 1-200 ADDRESS Baltimore MD 21205-2236, USA CONTACT help@gdb.org SITE ftp anonymous ftp.gdb.org SITE Directory / SITE-CONTACT help@gdb.org SITE gopher Host: gopher.gdb.org Port: 70 SITE URL gopher://gopher.gdb.org:/70/11/ SITE WWW Server at URL http://gdbwww.gdb.org/ 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 BC00447.1 NAME Dali server DOMAIN e-mail Server ANALYSIS DOMAIN Protein structure analysis DOMAIN Searching databases SERVER dali@embl-ebi.ac.uk DESCRIPTION The Dali server is a network service for comparing protein DESCRIPTION structures in 3D. You submit the coordinates of a query protein DESCRIPTION structure and Dali compares them against those in the Protein DESCRIPTION Data Bank. A multiple alignment of structural neighbours is DESCRIPTION mailed back to you. In favourable cases, comparing 3D structures DESCRIPTION may reveal biologically interesting similarities that are not DESCRIPTION detectable by comparing sequences. If you want to know the DESCRIPTION structural neighbours of a protein already in the Protein Data DESCRIPTION Bank, you can find them in the FSSP database. AUTHOR L. Holm, A. de Daruvar, C. Dodge, C. Sander RA Holm L., Sander C.; RT "Protein structure comparison by alignment of distance matrices."; RL J. Mol. Biol. 233:123-138(1993). RX Medline; 93389725. RX SeqAnalRef; HOLL9301. ADDRESS L. Holm, EMBL Outstation - EBI, The European Bioinformatics Institute, ADDRESS Cambridge CB10 1SD, United Kingdom CONTACT dali-help@embl-ebi.ac.uk SITE WWW Server at URL http://www2.embl-ebi.ac.uk/dali/ SITE-CONTACT - OS Unix LANGUAGE Perl,Fortran VOLUME - REQUIRES - AC BC00447.2 NAME Dali server DOMAIN e-mail Server ANALYSIS DOMAIN WWW Server DOMAIN Protein structure analysis DOMAIN Searching databases SERVER http://www.embl-ebi.ac.uk/dali/ DESCRIPTION The Dali server is a network service for comparing protein DESCRIPTION structures in 3D. You submit the coordinates of a query protein DESCRIPTION structure and Dali compares them against those in the Protein DESCRIPTION Data Bank. A multiple alignment of structural neighbours is DESCRIPTION mailed back to you. In favourable cases, comparing 3D structures DESCRIPTION may reveal biologically interesting similarities that are not DESCRIPTION detectable by comparing sequences. If you want to know the DESCRIPTION structural neighbours of a protein already in the Protein Data DESCRIPTION Bank, you can find them in the FSSP database. AUTHOR L. Holm, A. de Daruvar, C. Sander RA Holm L., Sander C.; RT "Protein structure comparison by alignment of distance matrices."; RL J. Mol. Biol. 233:123-138(1993). RX Medline; 93389725. RX SeqAnalRef; HOLL9301. ADDRESS L. Holm, EMBL Outstation - EBI, The European Bioinformatics Institute, ADDRESS Cambridge CB10 1SD, United Kingdom CONTACT dali-help@embl-ebi.ac.uk OS Unix,VMS LANGUAGE Perl,Fortran VOLUME - REQUIRES - AC BC00453 NAME EMBL-Search DOMAIN Searching databases DESCRIPTION EMBL-Search is a free database query and retrieval program for DESCRIPTION the MS Windows 3.x or greater for use with the EMBL Sequence DESCRIPTION Databases CD-ROM. Allows text queries of the PROSITE protein DESCRIPTION pattern database, in addition to the EMBL nucleotide, DESCRIPTION SWISS-PROT, LIGM. AUTHOR Matteo diTommaso ADDRESS EMBL outstation, Hinxton, EBI ADDRESS Hinxton Hall, Hinxton, Cambridge CB10 1RQ, UK CONTACT ditommaso@ebi.ac.uk SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/dos SITE-CONTACT nethelp@ebi.ac.uk SITE WWW Server at URL http://www.ebi.ac.uk OS MS Windows 3.x or greater LANGUAGE - VOLUME - REQUIRES EMBL Sequence database CD-ROM COMMENTS This program is used with the EMBL Sequence COMMENTS database CD-ROM COMMMENTS See entry BC00365 for the Macintosh version AC BC00458 NAME KabatMan DOMAIN WWW server DOMAIN Database and analysis DOMAIN Searching databases SERVER http://www.biochem.ucl.ac.uk/~martin/abs/simkab.html DESCRIPTION KabatMan is a database program for accessing the Kabat DESCRIPTION Antibody Sequence Database. Allows queries in a SQL-like DESCRIPTION query language or using a simple point and click interface. AUTHOR Andrew C.R. Martin RT - ADDRESS BSM Unit, Dept. Biochem. & Mol. Biol., ADDRESS University College London, ADDRESS Gower Street, ADDRESS London WC1E 6BT. ADDRESS U.K. CONTACT martin@biochem.ucl.ac.uk SITE WWW Server at URL http://www.biochem.ucl.ac.uk/~martin/abs/simkab.html OS - LANGUAGE - VOLUME - REQUIRES - 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 BC00475 NAME PSB (Prosite.doc Browser) DOMAIN Searching databases DESCRIPTION PSB V1.00 is a local browser for PROSITE.DOC database. DESCRIPTION It is possible to view/save/print every entry. DESCRIPTION Entries selectable by PDOC number or full name from a DESCRIPTION bidirectional linked list. Fast string searching on DESCRIPTION whole database (2 Mb) with an additional linked list DESCRIPTION for matching entries. DESCRIPTION Full multitasking, REXX port, OOP MUI-based fully DESCRIPTION configurable graphical user interface, on line bubble DESCRIPTION help, hypertext manual, automatic installer. DESCRIPTION Runs on every Amiga station with OS 3.x and MUI 3.x AUTHOR Stefano Peruzzi - University of Padua, Italy RT - ADDRESS Stefano Peruzzi ADDRESS University of Padua, Italy ADDRESS Ph. +39-49-8642711 CONTACT peru@maya.dei.unipd.it SITE WWW Server at URL http://ftp.wustl.edu/~aminet/ OS Amiga OS 3.x LANGUAGE C VOLUME 100 Kb + 2Mb for prosite.doc REQUIRES Amiga OS 3.x, MUI library 3.x COMMENTS Available at any AMINET site, CD, BBS COMMENTS ftp.unina.it/pub/aminet/misc/sci/PDB.lha COMMENTS ftp.uni-paderborn.de/pub/aminet/misc/sci/PSB.lha AC BC00481 NAME CDB (Chemical Database) DOMAIN Searching databases DOMAIN Chemistry DESCRIPTION CDB is a chemical database with a nice asynchronous DESCRIPTION OOP graphical user interface. Database is provided DESCRIPTION of full featured Rexx interface for reliable DESCRIPTION inter process communication and custom scripts. DESCRIPTION Fully configurable user interface, hypertext manual, DESCRIPTION bubble help, automatic installer. DESCRIPTION CDB runs on every Amiga station with OS 3.x and MUI 3.x. AUTHOR Stefano Peruzzi RT - ADDRESS Stefano Peruzzi ADDRESS University of Padua - Italy ADDRESS phone: +39-49-8642711 CONTACT peru@maya.dei.unipd.it CONTACT steve@amiga.dei.unipd.it SITE WWW Server at URL http://ftp.wustl.edu/~aminet/ OS Amiga OS 3.x LANGUAGE C VOLUME 40Kb REQUIRES Amiga OS 3.x, MUI library 3.x COMMENTS Available on any AMINET site, CD, BBS in directory COMMENTS "misc/sci", look for CDB.lha AC BC00483 NAME DBWATCHER DOMAIN Searching databases DOMAIN Alignment Search software DESCRIPTION DBWatcher is a program handling periodic BLAST searches to DESCRIPTION find similarities to your own sequences. It keeps track DESCRIPTION of the previous searches and only performs new ones when DESCRIPTION necessary (i.e. when the database has been updated, the DESCRIPTION sequence has been modified, or when settings have been DESCRIPTION changed). Only novel similarities are reported, thus DESCRIPTION saving the time of browsing through bulky result files. DESCRIPTION When executed daily (as a cron job) it ensures that you are DESCRIPTION informed as soon as new sequences similar to yours are DESCRIPTION incorporated into a given database. This is most valuable DESCRIPTION in association with an automatic database update DESCRIPTION procedure. Results are sent by electronic mail to one or DESCRIPTION several addresses making DBWatcher particularly suitable DESCRIPTION for collaborative database survey as well as for users who DESCRIPTION do not have access to locally maintained databases. DESCRIPTION From version 2.00, DBWatcher is also able to run as a DESCRIPTION Client of the NCBI BLAST Server for remote searches. AUTHOR Frederic Plewniak RT - ADDRESS CNRS - LGME 6520 ADDRESS I.G.B.M.C. ADDRESS B.P. 163 ADDRESS 67404 Illkirch Cedex - FRANCE CONTACT plewniak@igbmc.u-strasbg.fr SITE ftp anonymous ftp-igbmc.u-strasbg.fr SITE Directory /pub/DBWatcher SITE WWW server at http://www-igbmc.u-strasbg.fr/BioInfo/LocalDoc/DBWatcher SITE-CONTACT plewniak@igbmc.u-strasbg.fr OS Solaris, Digital Unix, Irix LANGUAGE ANSI C VOLUME <3Mb + log files REQUIRES BLAST programs and databases for local searches. REQUIRES NCBI ToolKit for remote searches as a BLAST Client. REQUIRES X/Motif libraries and the NCBI Vibrant ToolKit. COMMENTS The X and Vibrant libraries are only necessary for the COMMENTS companion program, SetDBwatcher, which provides a GUI COMMENTS to create and manage DBWatcher jobs. COMMENTS GCG's versions of the BLAST programs and databases can COMMENTS be used as well. 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 BC00496 NAME RNABOB DOMAIN RNA analysis DOMAIN Searching databases DESCRIPTION The program "rnabob" searches for RNA motifs in sequence databases. DESCRIPTION Rather than searching simply for primary sequence matches, rnabob DESCRIPTION allows one to search for secondary and tertiary structural motifs as DESCRIPTION well. DESCRIPTION DESCRIPTION The underlying algorithm is a non-deterministic finite state machine DESCRIPTION very similar to that used by UNIX regular expression pattern matching DESCRIPTION algorithms, but with the modification that downstream nodes may be DESCRIPTION constructed dynamically based on matches at upstream nodes (thus, the DESCRIPTION ability to search for complementarity or other absolute covariances). AUTHOR Sean R. Eddy RA Gautheret D., Major F. and Cedergren R.; RT "Pattern searching/alignment with RNA primary and secondary RT structures: an effective descriptor for tRNA."; RL Comp. Apps. Biosci. 6:325-331 (1990). RA Eddy S.R.; RT "RNABOB: a program to search for RNA secondary structure motifs in RT sequence databases."; RL Unpublished. ADDRESS Dept. of Genetics ADDRESS Washington University School of Medicine ADDRESS 660 S. Euclid Box 8232 ADDRESS St. Louis MO 63110, USA CONTACT eddy@genetics.wustl.edu SITE ftp anonymous genome.wustl.edu SITE Directory /pub/eddy/ SITE-CONTACT - OS Unix LANGUAGE C VOLUME - REQUIRES - AC BC00501 NAME WU-BLASTN DOMAIN Alignment Search software DOMAIN Searching databases DESCRIPTION Nucleotide query versus nucleotide sequence database search DESCRIPTION program, performing a 2-dimensional BLAST search with gaps DESCRIPTION and using Karlin-Altschul "Sum" statistics to evaluate DESCRIPTION the significance of the results; rapid and moderately sensitive; DESCRIPTION Washington University BLASTN version 2.0. AUTHOR Warren Gish RA Altschul S.F. and Gish W.; RT "Local alignment statistics."; RL Methods in Enzymology 266:460-80(1996). ADDRESS Dept. of Genetics ADDRESS Campus Box 8501 ADDRESS Washington University School of Medicine ADDRESS St. Louis MO 63108, USA CONTACT gish@watson.wustl.edu SITE WWW Server at URL http://blast.wustl.edu OS UNIX LANGUAGE C VOLUME - REQUIRES - COMMENTS No search services are provided by the WU-BLAST server. COMMENTS Users must download the software to run on their own server. AC BC00502 NAME WU-BLASTP DOMAIN Alignment Search software DOMAIN Searching databases DESCRIPTION Protein query versus protein sequence database search DESCRIPTION program, performing a 2-dimensional BLAST search with gaps DESCRIPTION and using Karlin-Altschul "Sum" statistics to evaluate DESCRIPTION the significance of the results; rapid and very sensitive; DESCRIPTION Washington University BLASTP version 2.0. AUTHOR Warren Gish RA Altschul S.F. and Gish W.; RT "Local alignment statistics."; RL Methods in Enzymology 266:460-80(1996). ADDRESS Dept. of Genetics ADDRESS Campus Box 8501 ADDRESS Washington University School of Medicine ADDRESS St. Louis MO 63108, USA CONTACT gish@watson.wustl.edu SITE WWW Server at URL http://blast.wustl.edu OS UNIX LANGUAGE C VOLUME - REQUIRES - COMMENTS No search services are provided by the WU-BLAST server. COMMENTS Users must download the software to run on their own server. AC BC00503 NAME WU-BLASTX DOMAIN Alignment Search software DOMAIN Searching databases DESCRIPTION Translated nucleotide query versus protein sequence database DESCRIPTION search program, performing a 2-dimensional BLAST search with DESCRIPTION gaps and using Karlin-Altschul "Sum" statistics to evaluate DESCRIPTION the significance of the results; rapid and moderately sensitive; DESCRIPTION Washington University BLASTX version 2.0. AUTHOR Warren Gish RA Altschul S.F. and Gish W.; RT "Local alignment statistics."; RL Methods in Enzymology 266:460-80 (1996). ADDRESS Dept. of Genetics ADDRESS Campus Box 8501 ADDRESS Washington University School of Medicine ADDRESS St. Louis MO 63108, USA CONTACT gish@watson.wustl.edu SITE WWW Server at URL http://blast.wustl.edu OS UNIX LANGUAGE C VOLUME - REQUIRES - COMMENTS No search services are provided by the WU-BLAST server. COMMENTS Users must download the software to run on their own server. AC BC00504 NAME WU-TBLASTN DOMAIN Alignment Search software DOMAIN Searching databases DESCRIPTION Protein query versus translated nucleotide sequence database DESCRIPTION search program, performing a 2-dimensional BLAST search with DESCRIPTION gaps and using Karlin-Altschul "Sum" statistics to evaluate DESCRIPTION the significance of the results; rapid and moderately sensitive; DESCRIPTION Washington University TBLASTN version 2.0. AUTHOR Warren Gish RA Altschul S.F. and Gish W.; RT "Local alignment statistics."; RL Methods in Enzymology 266:460-80(1996). ADDRESS Dept. of Genetics ADDRESS Campus Box 8501 ADDRESS Washington University School of Medicine ADDRESS St. Louis MO 63108, USA CONTACT gish@watson.wustl.edu SITE WWW Server at URL http://blast.wustl.edu OS UNIX LANGUAGE C VOLUME - REQUIRES - COMMENTS No search services are provided by the WU-BLAST server. COMMENTS Users must download the software to run on their own server. AC BC00505 NAME WU-TBLASTX DOMAIN Alignment Search software DOMAIN Searching databases DESCRIPTION Translated nucleotide query versus translated nucleotide sequence DESCRIPTION database search program, performing a 2-dimensional BLAST search DESCRIPTION with gaps and using Karlin-Altschul "Sum" statistics to evaluate DESCRIPTION the significance of the results; rapid and moderately sensitive; DESCRIPTION Washington University TBLASTX version 2.0. AUTHOR Warren Gish RA Altschul S.F. and Gish W.; RT "Local alignment statistics."; RL Methods in Enzymology 266:460-80(1996). ADDRESS Dept. of Genetics ADDRESS Campus Box 8501 ADDRESS Washington University School of Medicine ADDRESS St. Louis MO 63108, USA CONTACT gish@watson.wustl.edu SITE WWW Server at URL http://blast.wustl.edu OS UNIX LANGUAGE C VOLUME - REQUIRES - COMMENTS No search services are provided by the WU-BLAST server. COMMENTS Users must download the software to run on their own server. 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 BC00514 NAME HCDSearch DOMAIN Sequence tools DOMAIN Alignment Search software DOMAIN Searching databases DESCRIPTION The Human cDNA Database (HCD) at the Institute for Genomic DESCRIPTION Research (TIGR) is the most complete, non-redundant, and DESCRIPTION structured collection of human expressed DNA sequences DESCRIPTION available to date (1997). Sequences and other data can be DESCRIPTION retrieved by users having open an account at HCD/TIGR. DESCRIPTION A HCD search involves composing and sending queries one DESCRIPTION by one and this can become time consuming if many queries DESCRIPTION must be sent. Moreover, a large amount of time is required DESCRIPTION thereafter to process the results. The HCDSearch system DESCRIPTION automatically composes and sends the queries by electronic DESCRIPTION mail using information provided in a text file; it also DESCRIPTION greatly accelerates results processing, generating lists of DESCRIPTION HCD numbers and library identifiers in a format that renders DESCRIPTION them very easy to examine. The programs run on Unix platforms. AUTHOR Laurentiu COCEA RA Cocea L.; RL "Search the Human cDNA Database at TIGT."; RT Comput. Appl. Biosci. 13(2):201-204(1997). ADDRESS Institut National de la Sante et de la Recherche Medicale ADDRESS Unite 373 ADDRESS Faculte de Medecine Necker, 8e etage ADDRESS Universite Descartes ADDRESS 156 rue de Vaugirard ADDRESS 75730 Paris CEDEX 15 ADDRESS FRANCE CONTACT cocea@infobiogen.fr CONTACT cocea@necker.fr SITE ftp anonymous iubio.bio.indiana.edu SITE Directory molbio/search files: hcd-search* SITE files: hcd-search* SITE-CONTACT gilbertd@bio.indiana.edu OS UNIX LANGUAGE Pascal VOLUME archive approx. 300 Kbyte REQUIRES - COMMENTS Files: hcd-search.1.0.tar.Z and hcd-search.readme. COMMENTS Compiled for UNIX 5.4 on Sun SPARC 2000. 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 BC00539 NAME FAStRNA DOMAIN WWW server DOMAIN RNA analysis DOMAIN Searching databases SERVER http://www-igm.univ-mlv.fr/~mabrouk DESCRIPTION The FAStRNA program was defined to identify tRNA genes in DESCRIPTION complete genome sequences using a pattern matching approach. DESCRIPTION FAStRNA was tested on the yeast genome: less than 3 minutes DESCRIPTION were needed to scan both strands and results matched the DESCRIPTION annotations. AUTHOR Nadia El Mabrouk, Frederique Lisacek RA El Mabrouk N., Lisacek F. RT "Very fast identification of RNA lotifs in genomic DNA. RT Application to tRNA search in the yeast genome." RL J.Mol.Biol.264:46-55 (1996). ADDRESS N.El Mabrouk ADDRESS Institut G. Monge ADDRESS Universite de Marne-la-Vallee ADDRESS 93166 Noisy le Grand cedex, France ADDRESS F.Lisacek ADDRESS Laboratoire Genome et Informatique ADDRESS Universite de Versailles-Saint-Quentin ADDRESS 45 avenue des Etats-Unis ADDRESS 78035 Versailles cedex, France CONTACT mabrouk@monge.univ-mlv.fr CONTACT lisacek@genetique.uvsq.fr SITE WWW Server at URL http://www-igm.univ-mlv.fr/~mabrouk OS unix LANGUAGE C VOLUME - REQUIRES - 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 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 BC00582 NAME TargetFinder DOMAIN Searching databases DOMAIN Pattern Identification DOMAIN Genome Analysis DOMAIN WWW server SERVER http://hercules.tigem.it/TargetFinder.html DESCRIPTION Search for target genes of transcription factors DESCRIPTION TargetFinder is a new tool to facilitate database searches DESCRIPTION for candidate target genes of transcription factors. The DESCRIPTION use of this program allows to search a database of annotated DESCRIPTION sequences for binding sites located in context with other DESCRIPTION important transcription regulatory signals and regions, DESCRIPTION like the TATA element, the transcription start site, the DESCRIPTION promoter and so on, thereby greatly reducing the background DESCRIPTION usually associated with this kind of searches. AUTHOR Giovanni Lavorgna RA Lavorgna et al. RL Trends in Genetics 14:375-376(1998). RA Lavorgna et al, 1998. RL Bioinformatics, in press ADDRESS DIBIT-HSR ADDRESS Via Olgettina, 58 ADDRESS 20132 Milano Italy CONTACT giovanni.lavorgna@hsr.it SITE WWW Server at URL http://hercules.tigem.it/TargetFinder.html OS - LANGUAGE - VOLUME - REQUIRES - 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 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 -