Catalogue of Molecular Biology Programs Release 6.1 23 Jul 1999 All thanks are in the file biocatal.thanks. ===================================================================== AC BC00079 NAME BOB DOMAIN Alignment browser DESCRIPTION This tool will be most useful in an environment where a lot of DESCRIPTION Blast processing is done (for example cDNA projects). You can DESCRIPTION look at one or two results simultaneously (for example blastn DESCRIPTION and blastx). You can immediately view alignments, selectively DESCRIPTION choose what to save/print, etc. AUTHOR - RT - ADDRESS BioInformatics and Molecular Analysis Section (BIMAS), ADDRESS DSB, DCRT, NIH. CONTACT - SITE ftp anonymous ftp-bimas.dcrt.nih.gov SITE Directory /pub/bob SITE-CONTACT ftp-bimas@bimas.dcrt.nih.gov SITE gopher Host: megasun.bch.umontreal.ca Port: 70 SITE URL gopher://megasun.bch.umontreal.ca:70/11/CMB/Databases/Blast/BoB SITE-CONTACT Tim Littlejohn tim@bch.umontreal.ca OS Sun 4's running SunOS 4.1.x ,Hewlett Packard PA-RISC, HP/UX 9.x OS DECstations running Ultrix 4.3 , Convex C38 running ConvexOS 10.2 LANGUAGE C (+ X11R5 and Motif) VOLUME - COMMENTS Binaries are available and are compiled statically. COMMENTS The source code is also available. AC BC00080 NAME BTAB DOMAIN Alignment browser DESCRIPTION BLAST output parser AUTHOR Dubnick M. RA Dubnick M.; RT "Btab - A Blast Output Parser."; RL Comput. Appl. Biosci. 8:601-602(1992). RX Medline; 93105271. RX SeqAnalRef; DUBM9202. ADDRESS Receptor Biochemistry and Molecular Biology Section ADDRESS National Institute of Neurological Disorders and Stroke ADDRESS Park Building, Room 412, NIH ADDRESS Bethesda, MD 20892, USA ADDRESS Tel: 1-(301) 496-8800 CONTACT mdubnick@briggs.ninds.nih.gov 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 briggs.ninds.nih.gov SITE Directory /pub/btab SITE-CONTACT - OS Unix LANGUAGE C, yacc, lex VOLUME - AC BC00081 NAME TBOB DOMAIN Alignment browser DESCRIPTION Text based Blast Output Browser DESCRIPTION Output from the blast programs can be difficult to read, DESCRIPTION especially when there are many search results to be analysed, DESCRIPTION each potentially with many matches with sequences in the DESCRIPTION database.The output from blast is usually a long text file with DESCRIPTION information spread throughout it; as a consequence, viewing this DESCRIPTION output can be difficult and inconvenient. TBOB solves this DESCRIPTION problem by only showing parts of the blast output at any DESCRIPTION time,letting the user jump from one place to another using DESCRIPTION simple one-keystroke commands. DESCRIPTION TBOB also permits retrieval of sequences from the NCBI retrieve DESCRIPTION email server, so that interesting sequences can be obtained for DESCRIPTION further analysis. This is particularly convenient as it can be DESCRIPTION performed while the blast results are being viewed. DESCRIPTION TBOB has a character-based interface, and therefore no special DESCRIPTION graphical capabilities are needed. AUTHOR Pierre Rioux (riouxp@bch.umontreal.ca) RT - ADDRESS Organelle Genome Megasequencing Project ADDRESS Departement de Biochimie, Universite de Montreal ADDRESS C.P. 6128, Centre-ville, Montreal (Quebec), H3C 3J7, Canada CONTACT ogmp@bch.umontreal.ca SITE ftp anonymous megasun.bch.umontreal.ca SITE Directory /pub/tbob SITE gopher Host: megasun.bch.umontreal.ca Port: 70 SITE URL gopher://megasun.bch.umontreal.ca:70/11/CMB/Databases/Blast/tbob SITE-CONTACT Tim Littlejohn tim@bch.umontreal.ca OS Unix LANGUAGE Perl VOLUME - REQUIRES Perl 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 BC00445 NAME ANTHEPROT Web page DOMAIN WWW server DOMAIN Protein sequence analysis DOMAIN Structure prediction DOMAIN Pattern Identification DOMAIN Alignment browser SERVER http://www.ibcp.fr/predict.html DESCRIPTION ANTHEPROT is a server that allows to make: DESCRIPTION * Secondary structure predictions: GOR, DPM, HOMOLOGUE, SOPMA, DESCRIPTION Phd DESCRIPTION * Multiple alignment : Clustalw (Higgins), Multalin (Corpet) DESCRIPTION * Search for biological sites using PROSITE DESCRIPTION * Search for homologous protein : Program FASTA (W. Pearson) AUTHOR G. Deleage, C. Geourjon, C. Blanchet RA Geourjon C., Deleage G.; RT "SOPM: a self-optimised meyhod for protein secondary RT struture prediction."; RL Protein Eng. 7:157-164(1994) RX Medline; 94224747. RX SeqAnalRef; GEOC9302. RA Geourjon C., Deleage G.; RT "SOPMA:significant improvements in protein secondary RT structure prediction by consensus prediction from RT multiple alignments."; RL Comput. Appl. Biosci. 11(6):681-684(1995). ADDRESS Institut de Biologie et Chimie des Proteines ADDRESS IBCP-CNRS UPR 412, Groupe de modelisation et RMN ADDRESS 7, Passage du Vercors ADDRESS 69 367 Lyon cedex 07, FRANCE CONTACT deleage@ibcp.fr, geourjon@ibcp.fr SITE WWW server at URL http://www.ibcp.fr/predict.html SITE-CONTACT geourjon@ibcp.fr or deleage@ibcp.fr OS - LANGUAGE - VOLUME - REQUIRES - AC BC00448 NAME FSSP DOMAIN WWW server DOMAIN Protein structure analysis DOMAIN Alignment browser SERVER http://www.embl-heidelberg.de/dali/fssp/ DESCRIPTION Use WWW browsers to view fold classification DESCRIPTION and multiple structure alignments. AUTHOR L. Holm RA Holm L., Sander C.; RT The FSSP database of structurally aligned protein fold families. RL Nucleic Acids Res. 22:3600-3609(1994). RX Medline; 95023099. RX SeqAnalRef; HOLL9401. ADDRESS L. Holm, EMBL Outstation - EBI, Hinxton Hall, Cambridge CB10 1RQ, U.K. CONTACT dali-help@embl-heidelberg.de SITE WWW server at URL http://www.embl-heidelberg.de/dali/fssp/ SITE-CONTACT - OS - LANGUAGE Perl VOLUME - REQUIRES - AC BC00461 NAME DNA Stacks DOMAIN Sequence format conversion tools DOMAIN Sequence display DOMAIN Sequence editor DOMAIN Sequence analysis DOMAIN Sequence tools DOMAIN Protein sequence analysis DOMAIN Pattern Identification DOMAIN Alignment editing and display DOMAIN Alignment browser DOMAIN Genome Mapping Databases DOMAIN Phylogeny DESCRIPTION DNA Stacks (v. 1.1) is a HyperCard 2.x stack package DESCRIPTION for Macintosh computers featuring utilities for editing or DESCRIPTION coloring multiple DNA or protein sequence alignments, DESCRIPTION performing numerous data conversions or analyses related to DESCRIPTION molecular systematics, displaying auto-rescalable gene maps DESCRIPTION of mitochondrial or chloroplast genomes, extracting DNA DESCRIPTION gene sequences or translated protein sequences from about DESCRIPTION 26 animal mitochondrial genomes, and graphically depicting DESCRIPTION codon usage patterns. AUTHOR Eernisse, Douglas J. RA Eernisse, D. J.; RT "DNA Translator and Aligner: HyperCard utilities to aid RT phylogenetic analysis of molecules."; RL Comput. Appl. Biosci. 8:177-184(1992). RX Medline; 92274217. RX SeqAnalRef; EERD9201. ADDRESS D. J. Eernisse ADDRESS Dept. Biol. Sci. MH282 ADDRESS California State University ADDRESS Fullerton, CA 92634, USA CONTACT deernisse@fullerton.edu SITE ftp anonymous ftp.bio.indiana.edu SITE Directory /molbio/mac/ SITE-CONTACT archive@bio.indiana.edu SITE gopher Host: gopher://ftp.bio.indiana.edu Port: 70 SITE URL gopher://gopher://ftp.bio.indiana.edu:/70/11/IUBio-Software+Data/molbio/mac SITE WWW Server at URL http://biology.fullerton.edu/people/faculty/doug-eernisse/ OS MacOS LANGUAGE HyperTalk, C VOLUME 2 MB REQUIRES HyperCard 2.0 or greater, Macintosh AC BC00497 NAME Sequin DOMAIN Sequence format conversion tools DOMAIN Sequence display DOMAIN Sequence editor DOMAIN Sequence analysis DOMAIN Sequence tools DOMAIN Alignment editing and display DOMAIN Alignment browser DOMAIN Sequence data submissions DESCRIPTION Sequin is a stand-alone software tool developed by the NCBI DESCRIPTION for submitting entries to the GenBank, EMBL, or DDBJ DESCRIPTION sequence databases. It is capable of handling simple DESCRIPTION submissions which contain a single short mRNA sequence, and DESCRIPTION complex submissions containing long sequences, multiple DESCRIPTION annotations, segmented sets of DNA, or phylogenetic and DESCRIPTION population studies. AUTHOR Jonathan Kans, Colombe Chappey RT - ADDRESS NIH/NLM/NCBI ADDRESS Building 38A, Room 8N805 ADDRESS Bethesda, MD 20894 ADDRESS U.S.A. CONTACT info@ncbi.nlm.nih.gov SITE ftp anonymous ncbi.nlm.nih.gov SITE Directory /sequin SITE-CONTACT info@ncbi.nlm.nih.gov SITE WWW Server at URL http://www.ncbi.nlm.nih.gov/Sequin OS Mac (68K and PPC), Windows (16 and 32 bit), Unix (Sun, Solaris, SGI, Linux, DEC) LANGUAGE English VOLUME - REQUIRES - COMMENTS Information about this package is available from COMMENTS http://www.ncbi.nlm.nih.gov/Sequin AC BC00517 NAME ToPLign Toolbox for Protein aLignments DOMAIN Protein sequence analysis DOMAIN Alignment Search software DOMAIN Alignment editing and display DOMAIN Alignment browser DOMAIN WWW server SERVER http://cartan.gmd.de/ToPLign.html DESCRIPTION ToPLign implements standard pairwise and multiple alignment DESCRIPTION methods with flexible parameter handling. The analysis of DESCRIPTION alignments is supported by offering different DESCRIPTION visualisations of alignments. In addition, ToPLign DESCRIPTION includes innovative approaches to the parametric alignment DESCRIPTION problem and the threading problem. The development of the DESCRIPTION ToPLign package is part of the PROTAL project AUTHOR Heinz Mevissen, Ralf Thiele, Ralf Zimmer RA Mevissen H, Thiele, R., Zimmer, R., Lengauer, T.; RT "The ToPLign software environment - RT Toolbox for Protein ALignment"; RL Bioinformatics'94, IMB, Jena (1994). ADDRESS Heinz Mevissen ADDRESS Ralf Thiele ADDRESS Ralf Zimmer ADDRESS Thomas Lengauer ADDRESS German National Research Center for Information Technology ADDRESS Schloss Birlinghoven, D-53754 Sankt Augustin CONTACT Heinz-Theordor.Mevissen@gmd.de CONTACT Ralf.Thiele@gmd.de CONTACT Ralf.Zimmer@gmd.de SITE WWW Server at URL http://cartan.gmd.de/ToPLign.html OS - LANGUAGE - VOLUME - REQUIRES - AC BC00561 NAME ClustalX DOMAIN Alignment Search software DOMAIN Alignment browser DOMAIN Phylogeny DESCRIPTION ClustalX is a new windows interface for the ClustalW DESCRIPTION alignment program. The sequence alignment is displayed in a DESCRIPTION window on the screen, with pull-down menus providing all the options DESCRIPTION from ClustalW. DESCRIPTION DESCRIPTION New features: cut-and-paste operations; highlighting of DESCRIPTION conserved features; selection of a subset of sequences or a DESCRIPTION sub-range to be realigned; alignment quality analysis DESCRIPTION highlighting low-scoring regions. DESCRIPTION DESCRIPTION Available for SUN Solaris, SGI IRIX5, Digital UNIX for DEC, DESCRIPTION MS Windows (32 bit) for PC, Linux ELF for x86 PC, Macintosh DESCRIPTION PowerMac. AUTHOR Thompson J.D, Gibson T.J, Plewniak F, Jeanmougin F, Higgins D.G. RA Thompson J.D, Gibson T.J, Plewniak F, Jeanmougin F, Higgins D.G.; RA "The ClustalX windows interface: flexible strategies for RA multiple sequence alignment aided by quality analysis tools."; RL Nucleic Acids Res. 25:4876-4882(1997). ADDRESS IGBMC, ADDRESS Parc d'Innovation, ADDRESS Illkirch-Graffenstaden, ADDRESS France. CONTACT julie@igbmc.u-strasbg.fr SITE ftp anonymous ftp-igbmc.u-strasbg.fr SITE Directory pub/ClustalX SITE-CONTACT jeanmougin@igbmc.u-strasbg.fr OS UNIX,MS-Windows,Linux,MAC LANGUAGE C VOLUME - REQUIRES - COMMENTS Executables available for listed machines AC BC00563 NAME MView DOMAIN Alignment browser DESCRIPTION A tool for converting the results of a sequence database DESCRIPTION search into the form of a coloured multiple alignment of DESCRIPTION hits stacked against the query. Alternatively, an existing DESCRIPTION multiple alignment can be processed. In either case, the DESCRIPTION output is simply HTML, so the result is platform independent DESCRIPTION and requires no separate application or applet to be loaded. AUTHOR Nigel P. Brown RA Brown, N.P., Leroy, C., Sander, C. RT "MView: A Web compatible database search or multiple RT alignment viewer."; RL Bioinformatics (1998). ADDRESS European Bioinformatics Institute (EMBL-EBI), ADDRESS Wellcome Genome Campus, Cambridge, CB10 1SD, U.K. CONTACT brown@ebi.ac.uk SITE WWW Server at URL http://www.sander.ebi.ac.uk/mview/ OS UNIX LANGUAGE perl VOLUME 532k REQUIRES perl version 5.003 or higher 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 BC00588 NAME DAMBE (Data analysis in molecular biology and evolution) DOMAIN Sequence format conversion tools DOMAIN Sequence display DOMAIN Sequence analysis DOMAIN Sequence tools DOMAIN Protein sequence analysis DOMAIN Protein structure analysis DOMAIN Alignment editing and display DOMAIN Alignment browser DOMAIN Genetic tools DOMAIN Molecular Evolution DOMAIN Phylogeny DOMAIN Database and analysis DOMAIN Searching databases DOMAIN General tools DOMAIN Statistical significance DOMAIN Comparative analysis DESCRIPTION DAMBE (Data Analysis in Molecular Biology DESCRIPTION and Evolution) is an integrated software package for DESCRIPTION converting, manipulating, statistically and graphically DESCRIPTION describing and analyzing molecular sequence data, with a DESCRIPTION user-friendly Windows 95 interface. AUTHOR Xuhua Xia RT - ADDRESS Department of Ecology & Biodiversity, ADDRESS University of Hong Kong, Hong Kong CONTACT xxia@hkusua.hku.hk SITE WWW Server at URL http://web.hku.hk/~xxia/software/software.htm OS Windows 95 LANGUAGE - VOLUME 10 MB REQUIRES Windows 95 AC BC00590 NAME FASTA SCAN DOMAIN Sequence format conversion tools DOMAIN Sequence tools DOMAIN GCG tools DOMAIN Alignment editing and display DOMAIN Alignment browser DESCRIPTION FASTA SCAN allow you to select and save sequences of real DESCRIPTION interest from a FASTA output. DESCRIPTION This version was successfully tested with: DESCRIPTION - FASTA of GCG package (v.8.1 and 10) DESCRIPTION - FASTA of "Pearson package" version 3.1t07 May, 1998 DESCRIPTION The maximum number of sequences is 1000. AUTHOR Olivier Friard RT - ADDRESS Dipartimento di Genetica, Biologia e Biochimica ADDRESS via Santena, 5bis ADDRESS I-10126 TURIN ITALY CONTACT friard@molinette.unito.it SITE WWW Server at URL http://pcgen018.molinette.unito.it/programs.html OS win95, win98, NT 4.0 LANGUAGE - VOLUME - REQUIRES - AC BC00597 NAME NHGRI's WebBLAST DOMAIN Sequence analysis DOMAIN Protein sequence analysis DOMAIN Alignment browser DESCRIPTION WebBLAST 2.0 is a suite of Macintosh and UNIX programs intended to DESCRIPTION assist in organizing sequencing data as well as providing first-pass DESCRIPTION sequence analysis in an automated fashion. One of the main features of DESCRIPTION WebBLAST is that its system requirements are minimal, needing only DESCRIPTION MacPerl on the Macintosh client, Perl 5.004 and BLAST on the UNIX DESCRIPTION client, and a Web server. All output is viewed through a Web browser, DESCRIPTION allowing users to access the refined data regardless of platform. The DESCRIPTION software can be previewed and downloaded at DESCRIPTION http://genome.nhgri.nih.gov/webblast. DESCRIPTION DESCRIPTION Data enters the WebBLAST pipeline through the use of a MacPerl droplet DESCRIPTION on the Macintosh connected to the sequencer. The droplet transfers the DESCRIPTION data into the UNIX file system and places the data into a holding area DESCRIPTION on the server. A nightly cron job then invokes the automatic processing DESCRIPTION of new data: [1] Sequences are moved from the holding area to the DESCRIPTION appropriate directory within the UNIX file system. [2] Sequences are DESCRIPTION screened for the presence of vector, alu, and other repetitive DESCRIPTION sequences and masked. [3] Local BLAST searches are then run on the DESCRIPTION masked data, assessing each BLAST hit for statistical significance. [4] DESCRIPTION A CGI program generates HTML pages presenting the user with a summary DESCRIPTION table of hit counts as well as information on the significant hits. [5] DESCRIPTION Sequence data are re-BLASTed monthly against the NCBI month database, DESCRIPTION with any new hit information being appended to the summary pages of the DESCRIPTION appropriate sequence set; this assures that BLAST results are kept DESCRIPTION up-to-date. DESCRIPTION Once the sequence comparisons have been run, users can add comments to DESCRIPTION individual sequences that can be viewed by all users. Users can also DESCRIPTION view the associated sequence traces directly through the use of a Java DESCRIPTION applet. Each data set can be password protected, so that multiple DESCRIPTION projects can be supported while maintaining the integrity and security DESCRIPTION of the data. Data can be exported for use with assembly programs such DESCRIPTION as the PHRED/PHRAP/CONSED. As the programs are written in perl, users DESCRIPTION can easily modify the scripts to include additional analyses, such as DESCRIPTION performing BLAST runs against in-house data sets. AUTHOR Joseph Ryan, Erik Ferlanti, Izabela Makalowska, Andreas D. AUTHOR Baxevanis RT - ADDRESS - CONTACT webblaster@nhgri.nih.gov SITE WWW Server at URL http://genome.nhgri.nih.gov/webblast/ OS Unix LANGUAGE - VOLUME - REQUIRES NHGRI::Blastall, Perl AC BC00601 NAME Jalview DOMAIN Sequence display DOMAIN Sequence analysis DOMAIN Protein sequence analysis DOMAIN Alignment editing and display DOMAIN Alignment browser DOMAIN JAVA DOMAIN Multivariate analysis DOMAIN WWW server SERVER http://circinus.ebi.ac.uk:6543/jalview DESCRIPTION A multiple sequence alignment viewer and editor. Alignments DESCRIPTION can be divided into subfamilies using a tree or by hand. DESCRIPTION Conservation can then be calculated using physico-chemical DESCRIPTION properties within subfamilies or across the whole alignment. DESCRIPTION Principal component analysis can also be used as an DESCRIPTION alternative way of clustering the sequences. An SRS server DESCRIPTION can be used to fetch and display the sequence features and DESCRIPTION any PDB structures listed. There is limited access to DESCRIPTION external programs including clustalw and jnet secondary DESCRIPTION structure prediction. AUTHOR Michele Clamp RT - ADDRESS The Sanger Centre ADDRESS Wellcome Trust Genome Campus ADDRESS Hinxton ADDRESS Cambs. ADDRESS CB10 1SA ADDRESS UK CONTACT michele@sanger.ac.uk SITE WWW Server at URL http://circinus.ebi.ac.uk:6543/jalview OS - LANGUAGE java1.1 VOLUME 300kb REQUIRES Java runtime environment