Catalogue of Molecular Biology Programs Release 6.1 23 Jul 1999 All thanks are in the file biocatal.thanks. ===================================================================== AC BC00020 NAME BLIMPS DOMAIN Alignment Search software DOMAIN Database and analysis DESCRIPTION BLocks IMProved Searcher is a searching tool that scores DESCRIPTION a sequence against blocks or a block against sequences. DESCRIPTION BLIMPS augments the block functions of PATMAT for UNIX DESCRIPTION which is no longer supported by FHCRC AUTHOR Steven Henikoff & Jorja G. Henikoff RA Henikoff S., Henikoff J.G.: RT "Automated assembly of protein blocks for database searching"; RL Nucleic Acids Res. 19(23):6565-6572 (1991). RX Medline; 92093619. RX SeqAnalRef; HENS9101. ADDRESS Fred Hutchinson Cancer Research Center CONTACT - SITE ftp anonymous ncbi.nlm.nih.gov SITE Directory /repository/blocks/unix/blimps/ SITE-CONTACT federhen@ncbi.nlm.nih.gov (S Federhen ) SITE ftp anonymous howard.fhcrc.org SITE Directory /blimps OS - LANGUAGE C VOLUME - COMMENTS BLIMPS is also set up as part of the BLOCKS e-mail server COMMENTS Mail to blocks@howard.fhcrc.org with the subject line of COMMENTS "help" to find out more about the BLOCKS e-mail server. AC BC00097 NAME ACNUC DOMAIN Database and analysis DESCRIPTION ACNUC is a program to search sequences in the databanks. DESCRIPTION It reformats and index the database and provides DESCRIPTION a query program. AUTHOR Manolo Gouy. RA Gouy M., Gautier C., Attimonelli M., Lanave C., DiPaola G.; RT "ACNUC - a portable retrieval system for nucleic acid sequence RT databases: logical and physical designs and usage."; RL Comput. Appl. Biosci. 1:167-172(1985). RX Medline; 89208315. RX SeqAnalRef; GOUM8501. ADDRESS Universite Claude Bernard, Lyon, France CONTACT - SITE ftp anonymous biom3.univ-lyon1.fr SITE Directory /pub/acnuc SITE-CONTACT M Gouy : mgouy@evomol.univ-lyon1.fr OS Sun Unix, Vax/VMS LANGUAGE FORTRAN 77 VOLUME - AC BC00098 NAME GBSPLIT DOMAIN Database and analysis DESCRIPTION This is a small program for splitting GenBank update files DESCRIPTION into the different divisions AUTHOR Robert Jones RT - ADDRESS Thinking Machines Corporation, ADDRESS 245 First Street, Cambridge, MA 02142 , USA CONTACT jones@think.com SITE ftp anonymous think.com SITE Directory /think/genbank SITE-CONTACT - OS Unix LANGUAGE C VOLUME - REQUIRES - AC BC00099 NAME GBVECTOR DOMAIN Database and analysis DESCRIPTION This is a small program to uncover the presence of vector DESCRIPTION sequences in GenBank database entries AUTHOR Robert Jones RT - ADDRESS Thinking Machines Corporation, ADDRESS 245 First Street, Cambridge, MA 02142 , USA CONTACT jones@think.com SITE ftp anonymous think.com SITE Directory /think/genbank/gbvector SITE-CONTACT - OS Unix LANGUAGE C VOLUME - REQUIRES - AC BC00100 NAME HOVERGEN DOMAIN Database and analysis DESCRIPTION Homologous Vertebrate Genes Data Base DESCRIPTION HOVERGEN is a database of homologous vertebrate genes. DESCRIPTION HOVERGEN allows to easily select sets of homologous genes among DESCRIPTION a given set of vertebrate species. HOVERGEN contains all DESCRIPTION vertebrate sequences from GenBank (except ESTs), with some data DESCRIPTION corrected, clarified, or completed, notably to address the DESCRIPTION problem of redundancy. Coding sequences have been classified in DESCRIPTION gene families. Protein multiple alignments and phylogenetic DESCRIPTION trees have been calculated for each family. DESCRIPTION Sequences and related information have been structured in an DESCRIPTION ACNUC database. A program named "query" allows to make complex DESCRIPTION selections in the ACNUC database according to any information DESCRIPTION clearly declared (keywords, bibliography, taxonomy, etc.). DESCRIPTION Selection criteria can be combined with boolean operators. DESCRIPTION A graphical interface has been developed to visualize and edit DESCRIPTION trees. Genes are displayed in color, according to their taxonomy. DESCRIPTION Users have directly access to all information attached to DESCRIPTION sequences (either from GenBank or specific of HOVERGEN), or DESCRIPTION multiple alignments simply by clicking on genes. This graphical DESCRIPTION tool gives thus a rapid and simple access to all data necessary DESCRIPTION to interpret homology relationships between genes: phylogenetic DESCRIPTION trees of gene families, taxonomy, GenBank information and DESCRIPTION proteine multiple alignments. DESCRIPTION HOVERGEN is particularly useful for: DESCRIPTION - comparative sequence analysis DESCRIPTION - phylogeny DESCRIPTION - molecular evolution studies DESCRIPTION More generaly, HOVERGEN gives an overall view of what is known DESCRIPTION about a particular gene family. AUTHOR Laurent Duret RA Duret L., Mouchiroud D., Gouy M.; RT "HOVERGEN: a database of homologous vertebrate genes."; RL Nucleic Acids Res. 22:2360-2365(1994). RX Medline; 94310065. RX SeqAnalRef; DURL9401. AB This paper is available at the following AB URL http://biom1.univ-lyon1.fr/txtdoc/publint/duret.html ADDRESS Laboratoire de Biometrie, Genetique et Biologie des Populations ADDRESS UMR CNRS 5558 Universite Claude Bernard - Lyon I ADDRESS 43, Bd du 11 Novembre 1918 F-69622 Villeurbanne cedex FRANCE CONTACT - SITE ftp anonymous biom3.univ-lyon1.fr SITE Directory /pub/hovergen SITE-CONTACT Laurent Duret E-mail: duret@biomserv.univ-lyon1.fr SITE WWW server at URL http://biom1.univ-lyon1.fr/databases/hovergen.html SITE-CONTACT duret@biomserv.univ-lyon1.fr SITE ftp anonymous ncbi.nlm.nih.gov SITE Directory /repository/hovergen SITE-CONTACT NCBI E-mail: info@ncbi.nlm.nih.gov OS Present version runs on Sun workstations using SunOS or Solaris. OS Beta versions are available for: SGI, DecAlpha and IBM/RS6000. OS A color screen is recommended. LANGUAGE - VOLUME - AC BC00101 NAME NRDB DOMAIN Database and analysis DESCRIPTION used to generate the NCBI "nonredundant" DESCRIPTION databases. The NCBI locally builds a DESCRIPTION nonredundant protein sequence database from DESCRIPTION the PIR, SWISS-PROT, GenPept, and daily DESCRIPTION GenPept updates;a nonredundant nucleotide DESCRIPTION sequence database is built from the GenBank DESCRIPTION major quarterly release, GenBank daily DESCRIPTION updates, the EMBL Data Library, and the EMBL DESCRIPTION weekly updates: but the nrdb program will work DESCRIPTION with any input database(s) that are in FASTA/ DESCRIPTION Pearson format. AUTHOR Warren Gish RT - ADDRESS - CONTACT - SITE ftp anonymous ncbi.nlm.nih.gov SITE Directory /pub/nrdb SITE-CONTACT info@ncbi.nlm.nih.gov OS UNIX-compatible source code SUN SPARCstation, LANGUAGE C VOLUME - AC BC00102 NAME PROINDEX DOMAIN Database and analysis DESCRIPTION Index file creation for ProSite pattern database AUTHOR Clark S. RT - ADDRESS - CONTACT - SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/vax VAX software are stored as SITE uuencoded (.UUE) files. SITE-CONTACT nethelp@ebi.ac.uk OS VAX/VMS LANGUAGE FORTRAN VOLUME - AC BC00103 NAME PROSET DOMAIN Database and analysis DESCRIPTION program to create non-redundant DESCRIPTION sets of protein sequences AUTHOR Volker Brendel RT - ADDRESS - CONTACT - SITE ftp anonymous gnomic.stanford.edu SITE Directory /pub SITE-CONTACT - OS - LANGUAGE C VOLUME - 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 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 BC00385 NAME FlyView DOMAIN Database and analysis DOMAIN Genetic and Physical Mapping DESCRIPTION We are starting to construct an image database on Drosophila DESCRIPTION development and genetics, especially on expression patterns of DESCRIPTION genes (enhancer trap lines, cloned genes). Our aim is to DESCRIPTION establish the possibilty to compare images on the computer DESCRIPTION screen and to search for special patterns at different DESCRIPTION developmental stages. Therefore, all images are accompanied by DESCRIPTION text descriptions that can be used to search with keywords. DESCRIPTION Drosophila workers are asked to contribute to this database by DESCRIPTION submitting images and accompanying text. At the moment we can DESCRIPTION accept only digitalized images (sent by e-mail or on diskette). DESCRIPTION We hope to get financial support in the near future to offer a DESCRIPTION variety of other possibilities, for example acceptance of DESCRIPTION microscopic or photographic slides, reprints of publications or DESCRIPTION color prints of photographs. AUTHOR - RT - ADDRESS Westfälische Wilhelms-Universität Münster, ADDRESS Institut für Allgemeine Zoologie und Genetik, ADDRESS Arbeitsgruppe Entwicklungsgenetik ADDRESS Muenster, Germany CONTACT janning@vnwz00.uni-muenster.de SITE WWW Server at URL http://pbio07.uni-muenster.de/ SITE-CONTACT janning@vnwz00.uni-muenster.de OS - LANGUAGE - VOLUME - REQUIRES a WWW front-end wich supports forms (Mosaic, Netscape ..) AC BC00390 NAME YANK DOMAIN Database and analysis DESCRIPTION This is a retrieval system for entries inside a flat-file DESCRIPTION database. DESCRIPTION The system works with for any flat-file database system such as DESCRIPTION those used in the public DNA and protein archives. AUTHOR Owen White and Will FitzHugh RA White O., FitzHugh W.; RT "A rapid retrieval tool for operating on large RT flat archive files."; RL Comput. Appl. Biosci. 11:45-47(1995). RX SeqAnalRef; WHIO9501. ADDRESS The Institute for Genomic Research, 932 Clopper Rd, Gaithersburg, ADDRESS MD 20878, USA. CONTACT will@tigr.org and owhite@tigr.org SITE ftp anonymous ftp.tigr.org SITE Directory /pub/yank SITE-CONTACT will@tigr.org OS UNIX (tested on SunOS and Solaris) LANGUAGE C VOLUME 1MB disk space for applications. Index file space dependent VOLUME on data file size. REQUIRES C compiler 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 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 BC00427 NAME DataMinder DOMAIN Sequence format conversion tools DOMAIN Sequence display DOMAIN Sequence editor DOMAIN Oligomer design and synthesis DOMAIN Database and analysis DESCRIPTION DataMinder is a standalone data management program designed DESCRIPTION for molecular biologists. One can readily store and retrieve DESCRIPTION data about oligonucleotides, nucleic acid or protein DESCRIPTION sequences, recombinant DNA clones, cells, reagents and DESCRIPTION protocols .A number of utilities for data analysis are provided, DESCRIPTION including those for calculating the Tms of oligonucleotides and DESCRIPTION for the evaluation of oligonucleotides for use as DESCRIPTION hybridization probes or primers for DNA synthesis. A DESCRIPTION variety of sequence editing features including voice veri- DESCRIPTION fication and the ability to import and export sequence data DESCRIPTION in a variety of different formats are also provided.Context- DESCRIPTION sensitive help is provided. DataMinder is simple to use and to DESCRIPTION customize and allows for sharing of database information DESCRIPTION across a computer network. AUTHOR Karen Usdin RA Usdin K.; RT "Hypercard-based data management tools for molecular biologists."; RL Comput. Appl. Biosci. 8:107-111(1992). RX Medline; 92274208. RX SeqAnalRef; USDK9201. ADDRESS Building 8, Room 202 ADDRESS 8 Center DR MSC 0830 ADDRESS National Institutes of Health ADDRESS Bethesda, MD 20892-0830 ADDRESS U.S.A. CONTACT ku@helix.nih.gov SITE - SITE-CONTACT - OS MAC LANGUAGE C, hypertalk VOLUME - REQUIRES Mac SE or above, 2MB Ram 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 BC00457 NAME MatInd and MatInspector DOMAIN Sequence analysis DOMAIN Database and analysis DESCRIPTION MatInd is a simple but powerful method to derive a DESCRIPTION matrix description of a consensus from a number of short sequences DESCRIPTION on which the definition of an IUPAC code would be based. DESCRIPTION MatInspector is a program that uses a large library of predefined DESCRIPTION matrix descriptions of transcription factor binding sites DESCRIPTION to locate matches in nucleotide sequences of unlimited length. DESCRIPTION It assigns a quality rating to matches and thus allows a quality- DESCRIPTION based filtering and selection of matches. AUTHOR Quandt, K., Frech, K., Karas, H., Wingender, E., Werner, T. RA Quandt, K., Frech, K., Karas, H., Wingender, E., Werner, T.: RT "MatInd and MatInspector - New fast and versatile tools for RT detection of consensus matches in nucleotide sequence data."; RL Nucleic Acids Res. 23:4878-4884(1995). ADDRESS - CONTACT quandt@gsf.de SITE ftp anonymous ariane.gsf.de SITE Directory /pub SITE-CONTACT quandt@gsf.de SITE WWW Server at URL http://www.gsf.de./biodv/matinspector.html OS UNIX,DOS,MacOS LANGUAGE C VOLUME - REQUIRES - AC 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 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 BC00515 NAME DROSOPOSON DOMAIN Genetic tools DOMAIN Population Genetics DOMAIN Database and analysis DOMAIN Statistical significance DOMAIN Comparative analysis DESCRIPTION An object-oriented knowledge base dedicated DESCRIPTION on localisation data of transposable element insertions DESCRIPTION along the polytene chromosomes of Drosophila. The base DESCRIPTION brings together: DESCRIPTION 1) data available on chromosomal localisations of DESCRIPTION transposable element insertions and on features of the DESCRIPTION polytene chromosomes (DNA content, recombination rate, DESCRIPTION breakpoints...), 2) some statistical methods aimed at DESCRIPTION analysing the distribution of the transposable element DESCRIPTION insertions along the chromosomes, in relation with the DESCRIPTION chromosome features. DROSOPOSON can thus be used either as DESCRIPTION a consultation tool, as an instant look of the available DESCRIPTION knowledge, or to analyse user's data. AUTHOR Christine HOOGLAND RA Hoogland C., Biemont C.; RT "DROSOPOSON: a knowledge base on chromosomal localization of RT transposable element insertions in Drosophila."; RL Compu. Appl. Biosci. 13:61-68(1997). ADDRESS Laboratoire de Biometrie, Genetique et Biologie des populations ADDRESS UMR CNRS 5558 ADDRESS Universite C. Bernard - Lyon 1 ADDRESS 69622 Villeurbanne ADDRESS France CONTACT hoogland@biomserv.univ-lyon1.fr SITE ftp anonymous biom3.univ-lyon1.fr SITE Directory /pub/drosoposon SITE-CONTACT - OS Sun/Solaris LANGUAGE LE_LISP VOLUME - REQUIRES - COMMENTS Commercial softwares needed: Le_Lisp and Aida by ILOG (ILOG SA, Gentilly, France); COMMENTS Knowledge base manager: SHIRKA developed by INRIA and the ARTEMIS laboratory in Grenoble, COMMENTS France (Francois.Rechenmann@inria.fr). COMMENTS All the files (data, programs, schemes) are available independently, as plain text. AC BC531 NAME CLEANUP DOMAIN Database and analysis DESCRIPTION CLEANUP program implements a new algorithm based on DESCRIPTION an "approximate string matching" procedure, which is DESCRIPTION able to determine the overall degree of similarity DESCRIPTION between each pair of sequences contained in a nucleotide DESCRIPTION sequence database and to generate automatically DESCRIPTION nucleotide sequence collections purified from DESCRIPTION redundancies. AUTHOR Grillo,Attimonelli,Liuni,Pesole RA Grillo G., Attimonelli M., Liuni S., and Pesole G.; RT "CLEANUP: a fast computer program for removing redundancies RT from nucleotide sequence databases"; RL Comput. Appl. Biosci. 12:1-8 (1996). ADDRESS Sabino Liuni ADDRESS Area di Ricerca CNR ADDRESS Via Amendola 166/5 ADDRESS 70126 Bari (Italy) CONTACT sabino@area.ba.cnr.it SITE ftp anonymous area.ba.cnr.it SITE Directory pub/embnet/software/Cleanup SITE-CONTACT sabino@area.ba.cnr.it OS Unix LANGUAGE C VOLUME - REQUIRES - AC BC00546 NAME MOLE DOMAIN Protein structure analysis DOMAIN Molecular modelling and graphics DOMAIN Database and analysis DESCRIPTION Molecular Visualization and Modeling Tool for Windows 95/NT. DESCRIPTION Provides fast ane high quality 3-d graphics based on Open GL DESCRIPTION graphics API. Comes on the CDs bundled with Protein Data Bank. DESCRIPTION Regular updates are offered AUTHOR George Privalov, Natalia Kurochkina RT - ADDRESS Applied Thermodynamics LLC ADDRESS 222 Schilling Circle, suite 130 ADDRESS Hunt Valley, MD 21031 ADDRESS USA CONTACT info@mole3d.com SITE WWW Server at URL http://www.mole3d.com OS Windows 95, Windows NT LANGUAGE C++ VOLUME 12 Mb REQUIRES CD-ROM drive, 256 Colours Graphics or more 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 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