Catalogue of Molecular Biology Programs Release 6.1 23 Jul 1999 All thanks are in the file biocatal.thanks. ===================================================================== AC BC00003 NAME AMAS DOMAIN Alignment Search software DOMAIN WWW server SERVER http://geoff.biop.ox.ac.uk/servers/amas_server.html DESCRIPTION Analysis of Multiply Aligned Sequences DESCRIPTION This is a system for hierarchical alignment analysis based DESCRIPTION on physico-chemical properties AUTHOR Livingstone C.D. and Barton G. J RA Livingstone C.D., Barton G.J; RT "Protein Sequence alignments: a strategy for the hierarchical RT analysis of residue conservation"; RL Comput. Appl. Biosci. 9:745-756(1993). RX Medline; 94192013. RX SeqAnalRef; LIVC9301. ADRESS EMBL Outstation, the EBI ADRESS Wellcome Trust Genome Campus ADRESS Hinxton, Cambridge CB10 1SD, UK CONTACT Barton, G. J.: geoff@ebi.ac.uk SITE Register and download software from http://barton.ebi.ac.uk SITE WWW Server at URL http://barton.ebi.ac.uk/servers/amas_server.html SITE_CONTACT geoff@ebi.ac.uk OS Sun, SGI, ALPHA/VMS probably others LANGUAGE C VOLUME - AC BC00051 NAME MSA DOMAIN Alignment Search software DOMAIN WWW server SERVER http://ibc.wustl.edu/msa.html DESCRIPTION MSA will read a file containing several protein DESCRIPTION sequences and attempt to produce a DESCRIPTION multiple alignment of these sequences, which DESCRIPTION it will write to standard output. AUTHOR John Kececioglu, Stephen Altschul, David AUTHOR Lipman & Robert Miner AUTHOR (v2.0) Alejandro Schaffer, Sandeep Gupta & John Kececioglu RA Lipman D.J., Altschul S.F., Kececioglu J.D.; RT "A tool for multiple sequence alignment."; RL Proc. Natl. Acad. Sci. U.S.A. 86:4412-4415(1989). RX Medline; 89282782. RX SeqAnalRef; LIPD8901. RA Carrillo H., Lipman D.J.; RT "The Multiple Sequence Alignment Problem in Biology."; RL SIAM J. Appl. Math. 48:1073-1082(1988). RX SeqAnalRef; CARH8801. RA Altschul S.F., Lipman D.J.; RT "Trees, Stars, and Multiple Biological Sequence Alignment."; RL SIAM J. Appl. Math. 49:197-209(1989). RX SeqAnalRef; ALTS8901. RA Altschul S.F.; RT "Gap Costs for Multiple Sequence Alignment."; RL J. Theor. Biol. 138:297-309(1989). RX Medline; 90080895. RX SeqAnalRef; ALTS8903. RA Altschul S.F., Carroll R.J., Lipman D.J.; RT "Weights for Data Related by a Tree."; RL J. Mol. Biol. 207:647-653(1989). RX Medline; 89342453. RX SeqAnalRef; ALTS8902. RA Altschul S.F.; RT "Leaf Pairs and Tree Dissections."; RL SIAM J. Discrete Math. 2:293-299(1989). ADDRESS National Center for Biotechnology Information ADDRESS National Library of Medicine, Bldg. 38A, Room 8N-811 ADDRESS Bethesda, MD 20894, USA. CONTACT altschul@tech.nlm.nih.gov (v1.0) CONTACT schaffer@cs.rice.edu (v2.0) SITE ftp anonymous softlib.cs.rice.edu SITE Directory /pub/msa SITE-CONTACT - SITE WWW Server at URL http://ibc.wustl.edu/msa.html SITE-CONTACT Hugh Chou : hugh@wustl.edu OS UNIX LANGUAGE C VOLUME - AC BC00300 NAME BLOCKS - server DOMAIN e-mail Server ANALYSIS DOMAIN WWW server SERVER blocks@howard.fhcrc.org SERVER http://www.blocks.fhcrc.org/blocks_search.html DESCRIPTION Compares a protein or DNA sequence to the DESCRIPTION current database of protein blocks. Blocks DESCRIPTION are short multiply aligned ungapped DESCRIPTION segments corresponding to the most highly DESCRIPTION conserved regions of proteins. The BLOCKS DESCRIPTION database has been constructed by successive DESCRIPTION application of the automated PROTOMAT DESCRIPTION system to individual entries in the PROSITE DESCRIPTION catalog of protein groups keyed to the SWISS- DESCRIPTION PROT protein sequence database. You can also DESCRIPTION use this server to retrieve specifics blocks DESCRIPTION and PROSITE entries. AUTHOR B Alford, J Henikoff, S Henikoff RA Henikoff S., Henikoff J.G.; RT "Automated assembly of protein blocks for database searching."; RL Nucleic Acids Res. 19:6565-6572(1991). RX Medline; 92093619. RX SeqAnalRef; HENS9101. ADDRESS Fred Hutchinson Center, Seattle, USA CONTACT henikoff@howard.fhcrc.org SITE WWW Server at URL http://www.blocks.fhcrc.org/ SITE-CONTACT webmaster@www.blocks.fhcrc.org OS - LANGUAGE - VOLUME - COMMENTS Send a mail to blocks@howard.fhcrc.org with the word COMMENTS help on the subject line AC BC00330 NAME PredictProtein DOMAIN e-mail Server ANALYSIS DOMAIN WWW server SERVER predictprotein@embl-heidelberg.de SERVER http://www.embl-heidelberg.de/predictprotein/phd_pred.html DESCRIPTION Analyze a protein sequence and sends back a DESCRIPTION multiple sequence alignment performed by a DESCRIPTION weighted dynamic programming method, called MaxHom (1) DESCRIPTION and a secondary structure prediction DESCRIPTION produced by a profile network method called PHDsec (2). AUTHOR Burkhard Rost, Reinhard Schneider, Antoine de Daruvar & C. Sander RA (1) Sander C., Schneider R.; RT "Database of Homology-Derived Structures and RT the Structural Meaning of Sequence Alignment."; RL Proteins 9:56-68(1991). RX Medline; 91204686. RX SeqAnalRef; SANC9101. RA (2) Rost B., Sander C.; RT "Improved prediction of protein secondary structure RT by use of sequence profiles and neural networks."; RL Proc. Natl. Acad. Sci. U.S.A. 90:7558-7562(1993). RX Medline; 93361486. RX SeqAnalRef; ROSB9304. RA Rost B., Sander C.; RT "Prediction of protein secondary structure at better RT than 70% accuracy."; RL J. Mol. Biol. 232:584-599(1993). RX Medline; 93347244. RX SeqAnalRef; ROSB9302. RA Rost B., Sander C.; RT "Combining evolutionary information and neural networks RT to predict protein secondary structure."; RL Proteins 19:55-72(1994). RX Medline; 94344959. RX SeqAnalRef; ROSB9404. RA Rost B., Sander C.; RT "Conservation and prediction of solvent accessibility in protein RT families."; RL Proteins 20:216-226(1994). RX SeqAnalRef; ROSB9405. RX Medline; 95199230. RA Rost B., Casadio, Fariselli, Sander C.; RT "Transmembrane Helices predicted at 95% accuracy."; RL Protein Sci. 4:534-537(1995). RX Medline; 95315875. RX SeqAnalRef; ROSB9501. ADDRESS Protein Design Group ADDRESS European Biology Molecular Laboratory (EMBL) ADDRESS Heidelberg / Germany CONTACT predict-help@embl-heidelberg.de SITE WWW Server at URL http://www.embl-heidelberg.de/predictprotein/predictprotein.html SITE-CONTACT - OS - LANGUAGE - VOLUME - COMMENTS For the email server send help in the message for information. AC BC00391 NAME BCM Search Launcher DOMAIN WWW server DOMAIN Sequence format conversion tools DOMAIN Sequence analysis DOMAIN Protein sequence analysis DOMAIN Protein structure analysis DOMAIN Structure prediction DOMAIN Pattern Identification DOMAIN Alignment Search software DOMAIN Alignment editing and display DOMAIN Alignment browser DOMAIN Restriction maps DOMAIN Database and analysis DOMAIN Searching databases DOMAIN Statistical significance DOMAIN Comparative analysis SERVER http://www.hgsc.bcm.tmc.edu/SearchLauncher/ DESCRIPTION The BCM Search Launcher is an integrated set of World- DESCRIPTION Wide Web (WWW) pages that organize molecular biology- DESCRIPTION related search and analysis services available on the DESCRIPTION WWW by function, and provide a single point-of-entry for DESCRIPTION related searches. The Protein Sequence Search Page, for DESCRIPTION example, provides a single sequence entry form for DESCRIPTION submitting sequences to WWW servers that provide remote DESCRIPTION access to a variety of different protein sequence search DESCRIPTION tools, including BLAST, FASTA, Smith-Waterman, BEAUTY, DESCRIPTION PROSITE, and BLOCKS searches. Other Launch pages provide DESCRIPTION access to 1) nucleic acid sequence searches, 2) multiple DESCRIPTION and pairwise sequence alignments, 3) gene feature searches, DESCRIPTION 4) protein secondary structure prediction, and 5) DESCRIPTION miscellaneous sequence utilities (e.g., 6-frame DESCRIPTION translation). The BCM Search Launcher also provides a DESCRIPTION mechanism to extend the utility of other WWW services by DESCRIPTION adding supplementary hypertext links to results returned DESCRIPTION by remote servers. For example, links to the NCBI's DESCRIPTION Entrez database and to the Sequence Retrieval System DESCRIPTION (SRS) are added to search results returned by the NCBI's DESCRIPTION WWW BLAST server. These links provide easy access to DESCRIPTION auxiliary information, such as Medline abstracts, that DESCRIPTION can be extremely helpful when analyzing BLAST database DESCRIPTION hits. For new or infrequent users of sequence database DESCRIPTION search tools, we have pre-set the default search parameters DESCRIPTION to provide the most informative first-pass sequence DESCRIPTION analysis possible. We have also developed a batch client DESCRIPTION interface for Unix and Macintosh computers that allows DESCRIPTION multiple input sequences to be automatically searched as DESCRIPTION a background task, with the results returned as individual DESCRIPTION HTML documents directly to the user's system. AUTHOR Randall F. Smith, Brent A. Wiese, Mary K. Wojzynski, AUTHOR Daniel B. Davison , and Kim C. Worley RA Smith R.F., Wiese B.A., Wojzynski M.K., Davison D.B., Worley K.C.; RT "BCM Search Launcher--An integrated interface to molecular RT biology database search and analysis services available on RT the World-Wide Web."; RL Submitted. ADDRESS Randall F. Smith, Ph.D. ADDRESS Department of Molecular and Human Genetics, T-921, ADDRESS Baylor College of Medicine ADDRESS One Baylor Plaza, Houston, TX 77030, USA ADDRESS Tel: +1 (713) 798-4735 Fax: +1 (713) 798-5386 CONTACT rsmith@bcm.tmc.edu CONTACT kworley@bcm.tmc.edu SITE WWW Server at URL http://www.hgsc.bcm.tmc.edu/SearchLauncher/ SITE-CONTACT rsmith@bcm.tmc.edu SITE WWW Server at URL http://dot.imgen.bcm.tmc.edu:9331/downloads/software/batch_client.html SITE give information about the downloads SITE ftp anonymous dot.imgen.bcm.tmc.edu for a batch client SITE Directory /pub/software/search-launcher OS Unix and Macintosh for the batch client LANGUAGE Perl (on Unix), AppleScript (on Macintosh) VOLUME - REQUIRES MacTCP on Macintosh and AppleScript, Perl on Unix AC BC00392 NAME BLASTPAT and FASTPAT DOMAIN Protein sequence analysis DOMAIN Alignment Search software DOMAIN WWW server DESCRIPTION Pattern Database Search Tools for Fast and Sensitive Gene DESCRIPTION Function Identification. DESCRIPTION BLASTPAT and FASTPAT are tools designed to identify protein DESCRIPTION sequences whose functions are not identified by standard BLAST DESCRIPTION or FASTA database searches. These modified versions of BLAST and DESCRIPTION FASTA perform rapid and sensitive searches of our Pattern DESCRIPTION Induced Multiple Alignment (PIMA) Pattern Database. The PIMA DESCRIPTION Pattern Database contains 22,422 patterns generated from DESCRIPTION multiple sequence alignments of 12,669 protein families we have DESCRIPTION identified in the NCBI's Entrez protein sequence database. DESCRIPTION Patterns in the PIMA database are encoded by a maximized DESCRIPTION information content alphabet. This extended alphabet includes DESCRIPTION the standard 20 letter IUPAC amino acid codes plus 61 other DESCRIPTION characters (lowercase characters, digits, other symbols) DESCRIPTION representing those combinations of residues which contribute the DESCRIPTION highest information as observed across all aligned positions in DESCRIPTION our protein family alignments. Pattern database searches are DESCRIPTION performed using new log-odds scoring matrices that we have DESCRIPTION developed for use with this new extended alphabet. In contrast DESCRIPTION to standard scoring matrices like PAM or BLOSUM, these new DESCRIPTION pattern-based matrices distinguish between conserved and DESCRIPTION variable positions, increasing search sensitivity and DESCRIPTION selectivity DESCRIPTION A more detailed description of these program is available at: DESCRIPTION http://dot.imgen.bcm.tmc.edu:9331/seq-search/Help/blastpat.html DESCRIPTION http://dot.imgen.bcm.tmc.edu:9331/seq-search/Help/fastpat.html AUTHOR Istvan Ladunga, Brent Wiese, and Randall F. Smith RT - ADDRESS Human Genome Center, Department of Molecular and Human Genetics ADDRESS and W.M. Keck Center for Computational Biology ADDRESS Baylor College of Medicine, Houston, TX 77030, USA ADDRESS tel: +1 713-798-8089 - fax: +1 713-798-5386 CONTACT {istvanl,brent,rsmith}@bcm.tmc.edu SITE WWW Server at URL http://gc.bcm.tmc.edu:8088/search-launcher/launcher.html OS - LANGUAGE - VOLUME - REQUIRES - AC 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 BC00417 NAME EBI/EMBL sequence data submission system DOMAIN Sequence data submissions DOMAIN WWW server SERVER http://www.ebi.ac.uk/subs/emblsubs.html DESCRIPTION An object oriented system that generates a sequence of forms DESCRIPTION to collect sequence information for the EMBL database. The system DESCRIPTION checks and validates the information and provides the ability DESCRIPTION to correct each data item. Details can be pre-filled according DESCRIPTION to a previous accession number, and can be saved for further DESCRIPTION use between various submissions. DESCRIPTION It is compatible with all known WWW browsers currently available DESCRIPTION including lynx. DESCRIPTION The system is generic in nature and will be used in the near future DESCRIPTION for other submission systems. AUTHOR Benny Shomer RA Flores, T.P., Shomer, B.; RT "The European Bioinformatics Institute: Submission and RT Updating of Sequence Databases."; RL Submitted for Publication. ADDRESS External Biological Liaison Officer, ADDRESS EMBL outstation - The EBI, ADDRESS Hinxton Hall, Hinxton,Cambridge CB10 1RQ, UK CONTACT bshomer@EBI.ac.uk SITE WWW Server at URL http://www.ebi.ac.uk/ SITE-CONTACT nethelp@ebi.ac.uk OS UNIX LANGUAGE Python VOLUME - REQUIRES A Python interpreter COMMENTS Parts of the source code will be made available for the public COMMENTS in the future. AC BC00423 NAME Pol3scan DOMAIN WWW server DOMAIN Sequence analysis SERVER http://irisbioc.bio.unipr.it/genomics.html DESCRIPTION Recognition of the eukaryotic internal control regions DESCRIPTION A box and B box that are typical of tRNA genes and DESCRIPTION tDNA-derived elements. The algorithm is based on the DESCRIPTION statistical analysis of a database of 231 tRNA DESCRIPTION promoter regions and makes use of weight matrices and DESCRIPTION weight vectors for scoring. The program discriminates DESCRIPTION between tRNA genes and related class III elements DESCRIPTION (e.g. tDNA-derived SINEs) on the basis of the presence DESCRIPTION of a transcriptional terminator signal and of the DESCRIPTION base-pairing within the aminoacyl stem. The accuracy DESCRIPTION of the prediction was estimated by scanning the DESCRIPTION eukaryotic nuclear sequences present in the rel. 33 of DESCRIPTION the EMBL database (65180 entries). The program DESCRIPTION correctly identified 932 of 940 known tRNA genes DESCRIPTION (0.85% of false negatives) with a false positive rate DESCRIPTION of 0.0018%. AUTHOR Pavesi A., Percudani R., Ottonello S.; RA Pavesi A., Conterio F., Bolchi A., Dieci G., and Ottonello S.; RT "Identification of new eucariotic tRNA genes in genomic databases RT by a multi weight matrix analysis of transcriptional control RT regions."; RL Nucleic Acids Res. 22:1247-1256 (1994). RX Medline; 94218250. RX SeqAnalRef; PAVA9401. ADDRESS Institute of Biochemical Sciences ADDRESS University of Parma ADDRESS Viale delle Scienze ADDRESS 43100 Parma, Italy CONTACT riccardo@irisbioc.bio.unipr.it SITE WWW Server at URL http://irisbioc.bio.unipr.it/pol3scan.html OS DOS,Unix LANGUAGE C VOLUME - REQUIRES - AC BC00428 NAME POLYAH, TSS, TSSG DOMAIN Sequence analysis DOMAIN e-mail Server ANALYSIS DOMAIN WWW server SERVER http://dot.imgen.bcm.tmc.edu:9331/gene-finder/gf.html SERVER service@bchs.uh.edu SERVER services@bioinformatics.weizmann.ac.il DESCRIPTION Analysis of uncharacterized human sequences DESCRIPTION TSSG and TSSW Recognition of human PolII promoter region DESCRIPTION and start of transcription. AUTHOR - RT - ADDRESS The Baylor College Of Medicine Computational Biology Group ADDRESS Houston, TX CONTACT solovyev@cmb.bcm.tmc.edu SITE WWW Server at URL http://dot.imgen.bcm.tmc.edu:9331/gene-finder/gf.html OS - LANGUAGE - VOLUME - REQUIRES - AC 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 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 BC00450 NAME MaxSprout DOMAIN WWW server DOMAIN Structure prediction SERVER http://www2.ebi.ac.uk/dali/maxsprout/maxsprout_request.html DESCRIPTION MaxSprout is a fast database algorithm for generating protein DESCRIPTION backbone and side chain co-ordinates from a C(alpha) trace. The DESCRIPTION backbone is assembled from fragments taken from known DESCRIPTION structures. Side chain conformations are optimized in rotamer DESCRIPTION space using a rough potential energy function to avoid clashes. AUTHOR A. de Daruvar, L. Holm, C. Sander RA Holm L., Sander C.; RT "Database algorithm for generating protein backbone and RT side-chain co-ordinate from a C-alpha trace."; RL J. Mol. Biol. 218:183-194(1991). RX Medline; 91162641. RX SeqAnalRef; HOLL9101. 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://www2.ebi.ac.uk/dali/maxsprout/ SITE-CONTACT - OS VMS LANGUAGE Pascal,Fortran VOLUME - REQUIRES - AC BC00452 NAME FSED DOMAIN WWW server DOMAIN Sequence analysis DOMAIN Sequence tools SERVER http://ir2lcb.cnrs-mrs.fr/d_fsed/fsed.html DESCRIPTION FSED has been developed to detect frameshift errors on new sequences. DESCRIPTION It is a more general approach than the one described before (Posfai and DESCRIPTION Roberts (1992). Proc. Natl. Acad. Sci. USA, 89: 4698-4702; Claverie DESCRIPTION (1993) J. Mol. Biol. 234: 1140-1157), as it does not rely on similarity DESCRIPTION searches. The method is based on the hypothesis that the coding DESCRIPTION constraints induce a statistical bias in the distribution of the DESCRIPTION 3-tuples and 6-tuples in the three frames of an open reading frame. DESCRIPTION This bias is used to derive discriminant functions on a learning set DESCRIPTION of sequences by applying a correspondence analysis. DESCRIPTION The method has been extensively tested on simulated frameshift errors DESCRIPTION and the results obtained have shown that its sensitivity and its DESCRIPTION selectivity rely upon the bias of the k-tuple distribution observed DESCRIPTION in the analyzed sequences. AUTHOR Fichant Gwennaele, Quentin Yves RA Fichant G., Quentin Y.; RT "A frameshift error detection algorithm for DNA sequencing projects."; RL Nucleic Acids Res. 23:2900-2908(1995). ADDRESS Dr. Gwennaele Fichant ADDRESS Institut de Genetique et Microbiologie ADDRESS Batiment 400 ADDRESS Centre Universitaire d'Orsay ADDRESS 91405 Orsay Cedex, France CONTACT gaf@igmors.u-psud.fr CONTACT quentin@lcb.cnrs-mrs.fr SITE WWW Server at URL http://ir2lcb.cnrs-mrs.fr/ SITE-CONTACT quentin@lcb.cnrs-mrs.fr OS - LANGUAGE - VOLUME - REQUIRES - AC 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 BC00498 NAME Map123d SERVER http://www-bio.lirmm.fr:8090/map123d.html DOMAIN WWW server DOMAIN Protein sequence analysis DOMAIN Protein structure analysis DOMAIN Structure prediction DOMAIN Alignment editing and display DOMAIN Molecular modelling and graphics SERVER http://www-bio.lirmm.fr:8090/map123d.html DESCRIPTION This server offers a set of tools for protein homology modelling. DESCRIPTION The "introduction" page provides a short overview on the DESCRIPTION problem of homology modelling and presents the tools DESCRIPTION available in this server: DESCRIPTION - Global multiple Alignment DESCRIPTION - Secondary structure prediction DESCRIPTION - Evaluation of a structural model AUTHOR H. Ripoche, J. Gracy, L. Chiche RT - ADDRESS LIRMM ADDRESS 161, Rue Ada ADDRESS 34392 MONTPELLIER Cedex 5 - France CONTACT hr@lirmm.fr SITE WWW Server at URL http://www-bio.lirmm.fr:8090/map123d.html OS - LANGUAGE - VOLUME - REQUIRES Java compatible browser (e.g. Netscape 2.0 or above) REQUIRES for some of the tools AC BC00516 NAME RDP Recursive Dynamic Programming DOMAIN Structure prediction DOMAIN Alignment Search software DOMAIN WWW server SERVER http://cartan.gmd.de/ToPLign.html DESCRIPTION Protein Fold Prediction and Sequence-structure Alignment for DESCRIPTION Protein Sequences based on Aminoacidpair Interaction Potentials AUTHOR Ralf Thiele, Ralf Zimmer RA Thiele, R., Zimmer, R., Lengauer, T.; RT "Recursive Dynamic Programming for Adaptive RT Sequence and Structure Alignment"; RL Proc. of the Third International Conference on Intelligent RL Systems for Molecular Biology, 384-392(1995). ADDRESS Ralf Thiele Ralf Zimmer Thomas Lengauer ADDRESS German National Research Center for Information Technology ADDRESS Schloss Birlinghoven, D-53754 Sankt Augustin 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 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 BC00518 NAME 123D DOMAIN Structure prediction DOMAIN Alignment Search software DOMAIN WWW server SERVER http://cartan.gmd.de/ToPLign.html DESCRIPTION Protein Fold Prediction and Sequence-structure Alignment for DESCRIPTION Protein Sequences based on Contact Capacity Potentials AUTHOR Ralf Zimmer, Nick Alexandrov RA Alexandrov N., Nussinov R., Zimmer R.; RT "Fast Protein Fold Recognition via Sequence to RT Structure Alignment and Contact Capacity Potentials"; RL Proceedings of the First Pacific Symposium on Biocomputing, RL 53-72 (1996) ADDRESS Ralf Zimmer ADDRESS German National Research Center for Information Technology ADDRESS Schloss Birlinghoven, D-53754 Sankt Augustin ADDRESS Nick Alexandrov ADDRESS Amgen Inc. ADDRESS Thousands Oaks, CA, USA CONTACT Ralf.Zimmer@gmd.de SITE WWW Server at URL http://cartan.gmd.de/ToPLign.html OS - LANGUAGE - VOLUME - REQUIRES - AC BC00522 NAME Primers! for the WWW DOMAIN Sequence analysis DOMAIN Genetic tools DOMAIN Oligomer design and synthesis DOMAIN WWW server SERVER http://www.williamstone.com/primers DESCRIPTION Free oligonucleotide design and analysis online. AUTHOR Richard Resnick, Williamstone Enterprises Inc. RA Resnick, R.; RT "Primers! for the WWW"; RL http://www.williamstone.com (1997). ADDRESS 46A Cedar St. ADDRESS Waltham, MA 02154 CONTACT rjr@williamstone.com SITE WWW Server at URL http://www.williamstone.com/primers OS All LANGUAGE Perl VOLUME n/a REQUIRES Any Graphical WWW Browser AC 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 BC00526 NAME WebMol DOMAIN Protein structure analysis DOMAIN Molecular modelling and graphics DOMAIN WWW server DOMAIN JAVA SERVER http://www.embl-heidelberg.de/cgi/viewer.pl DESCRIPTION WebMol is a Java based program to display and analyze DESCRIPTION molecular structures stored in PDB format. The program DESCRIPTION comprises numerous graphical options as well as analysis DESCRIPTION tools as, for instance, Ramachandran and distance matrix DESCRIPTION plots, helix-helix packing geometrical analysis, detection DESCRIPTION of cavities, steric conflicts and others. AUTHOR Dirk Walther RA Walther D. (1997) RT "WebMol - a Java based PDB viewer."; RL Trends Biochem Sci, 22: 274-275(1997). ADDRESS Dirk Walther, PhD ADDRESS University of California, San Francisco ADDRESS Department of Cellular and Molecular Pharmacology ADDRESS San Francisco, CA 94143-0450, USA ADDRESS email: walther@cmpharm.ucsf.edu ADDRESS http://www.cmpharm.ucsf.edu/~walther/ CONTACT walther@cmpharm.ucsf.edu SITE WWW Server at URL http://www.embl-heidelberg.de/cgi/viewer.pl OS - LANGUAGE JAVA VOLUME - REQUIRES Java capable WWW-browser/ Java runtime system (stand-alone version) COMMENTS A stand-alone version is available from the server. AC BC00527 NAME tRNAscan-SE DOMAIN Sequence analysis DOMAIN RNA analysis DOMAIN WWW server DOMAIN Statistical significance SERVER http://genome.wustl.edu/eddy/tRNAscan-SE/ DESCRIPTION tRNAscan-SE identifies transfer RNA genes in genomic DNA or DESCRIPTION RNA sequences. It combines the specificity of the Cove DESCRIPTION probabilistic RNA prediction package (Eddy & Durbin, 1994) DESCRIPTION with the speed and sensitivity of tRNAscan 1.3 (Fichant & DESCRIPTION Burks, 1991) plus an implementation of an algorithm described DESCRIPTION by Pavesi and colleagues (1994) which searches for DESCRIPTION eukaryotic pol III tRNA promoters. tRNAscan-SE identifies DESCRIPTION 99-100% of transfer RNA genes in DNA sequence while giving DESCRIPTION less than one false positive per 15 gigabases. The program DESCRIPTION searches at approximately 30,000 bp per second. Other DESCRIPTION features include prediction of tRNA secondary structure, DESCRIPTION and detection of unusual tRNA homologues such as DESCRIPTION selenocysteine tRNAs, tRNA-derived repetitive elements and DESCRIPTION tRNA pseudogenes. AUTHOR Todd M. Lowe, Sean R. Eddy RA Lowe T.M., Eddy S.R.; RT "tRNAscan-SE: a program for improved detection RT of transfer RNA genes in genomic sequence."; RL Nucleic Acids Res 25: 955-964 (1997). RA Eddy, S.R., Durbin, R.; RT "RNA Sequence Analysis Using Covariance Models"; RL Nucleic Acids Res. 22: 2079-2088 (1994). RA Fichant G.A., Burks C.; RT "Identifying potential tRNA genes in genomic RT DNA sequences"; RL J Mol Biol 220: 659-671 (1991). RA Pavesi A., Conterio F., Bolchi A., Dieci G., RA Ottonello S.; RT "Identification of new eukaryotic tRNA genes in RT genomic databases by a multistep weight matrix RT analysis of transcriptional control regions."; RL Nucleic Acids Res. 22:1247-1256 (1994). ADDRESS Dept. of Genetics ADDRESS Washington University School of Medicine ADDRESS 660 S. Euclid, Box 8232 ADDRESS St. Louis MO 63110 CONTACT lowe@genetics.wustl.edu SITE WWW Server at URL http://genome.wustl.edu/eddy/tRNAscan-SE/ OS UNIX LANGUAGE C, Perl VOLUME - REQUIRES Perl 5.0+ AC BC00528 NAME Bielefeld University Bioinformatics Server DOMAIN Sequence analysis DOMAIN Sequence tools DOMAIN Protein sequence analysis DOMAIN Alignment Search software DOMAIN Genetic tools DOMAIN Phylogeny DOMAIN WWW server SERVER http://bibiserv.TechFak.Uni-Bielefeld.DE/ DESCRIPTION BibiServ is both, a fast computer to run web-based DESCRIPTION bioinformatics software and an integration point for DESCRIPTION the bioinformatics activities at Bielefeld University. AUTHOR multiple authors RT - ADDRESS University of Bielefeld ADDRESS Technische Fakultaet, AG PI ADDRESS PB 100 131 ADDRESS D - 33501 Bielefeld ADDRESS Germany CONTACT bibi@TechFak.Uni-Bielefeld.DE SITE WWW Server at URL http://bibiserv.TechFak.Uni-Bielefeld.DE/ OS any LANGUAGE English VOLUME - REQUIRES Netscape Navigator > 3.0 AC BC00529 NAME The USC Sequence Alignment Package DOMAIN Sequence analysis DOMAIN Sequence tools DOMAIN Protein sequence analysis DOMAIN Pattern Identification DOMAIN Alignment Search software DOMAIN Statistical significance DOMAIN WWW server SERVER http://www-hto.usc.edu/software/seqaln/ DESCRIPTION This library of functions aligns nucleotide and DESCRIPTION protein sequences finding global, local, overlapping, DESCRIPTION and fitting regions of alignment using the generalized DESCRIPTION Smith-Waterman linear gap function g(k) = DESCRIPTION a + b(k-1) with one or two DNA, RNA or one-letter coded protein sequences. Also finds DESCRIPTION statistical significance of local alignments using the Poisson clumping heuristic. DESCRIPTION DESCRIPTION The package also includes GFSR, a good pseudorandom number generator, and standalone DESCRIPTION programs to perform global, local, fit and overlap alignments. AUTHOR Paul Hardy, Michael S. Waterman RT - ADDRESS Department of Mathematics ADDRESS University of Southern California ADDRESS 1042 W. 36th Place, DRB 155 ADDRESS Los Angeles, CA 90089-1113 CONTACT phardy@hto.usc.edu SITE WWW Server at URL http://www-hto.usc.edu/software/seqaln/ OS - LANGUAGE C VOLUME - REQUIRES - AC BC00538 NAME DRAWHCA SERVER http://www.lmcp.jussieu.fr/~mornon DOMAIN WWW server DOMAIN Protein sequence analysis DOMAIN Protein structure analysis DESCRIPTION This WWW page enables you to draw an HCA (Hydrophobic Cluster DESCRIPTION Analysis)plot using the program drawhca. This server provides DESCRIPTION plots as colour or b&w PostScript files. AUTHOR Luc Canard, Alain Soyer RT - ADDRESS Jean-Paul Mornon ADDRESS Laboratoire de Mineralogie-Cristallographie - CNRS URA09 ADDRESS Universite Pierre et Marie Curie ADDRESS Tour 16, 2e etage, Boite 115 ADDRESS 4, place Jussieu ADDRESS F-75252 PARIS CEDEX 05 ADDRESS FRANCE CONTACT mornon@lmcp.jussieu.fr SITE WWW Server at URL http://www.lmcp.jussieu.fr/~mornon/ OS - LANGUAGE - VOLUME - REQUIRES - AC 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 BC00549 NAME k2d DOMAIN Protein structure analysis DOMAIN Neural Networks DOMAIN WWW server SERVER http://kal-el.ugr.es/k2d/spectra.html DESCRIPTION Algorithm for the estimation of the percentages of DESCRIPTION protein secondary structure from UV circular dichroism DESCRIPTION spectra using a Kohonen neural network with a 2-dimensional DESCRIPTION output layer. You can either use k2d via a web server or DESCRIPTION get the program and run it on your machine. AUTHOR M.A. Andrade, P. Chacon, J.J. Merelo, F. Moran RA Andrade, M.A., Chacon P., Merelo J.J and Moran F.; RT "Evaluation of secondary structure of proteins from RT UV circular dichroism using an unsupervised learning RT neural network."; RL Prot. Eng. 6:383-390(1993). RA Merelo, J.J., Andrade M.A., Prieto A. and Moran F.; RT "Proteinotopic Feature Maps."; RL Neurocomputing. 6:443-454(1994). ADDRESS Miguel A. Andrade ADDRESS EMBL Outstation - European Bioinformatics Institute, ADDRESS Wellcome Trust Genome Campus ADDRESS Hinxton, Cambridge CB10 1SD, UK CONTACT andrade@ebi.ac.uk SITE WWW Server at URL http://kal-el.ugr.es/k2d/spectra.html SITE-CONTACT andrade@ebi.ac.uk OS Unix, DOS LANGUAGE C VOLUME 4Mb REQUIRES - COMMENTS More information at COMMENTS http://columba.ebi.ac.uk:8765/~andrade/k2d.html AC BC00551 NAME The Gene Discovery Page DOMAIN WWW server DOMAIN Sequence tools DOMAIN Protein sequence analysis DOMAIN Genome Analysis SERVER http://www.geocities.com/CapeCanaveral/1915/gdp.html DESCRIPTION The purpose of this page is to serve as a "desktop" area, DESCRIPTION primarily for the bench scientist with little biocomputing DESCRIPTION background. It organizes existing search engines in a DESCRIPTION coherent, stepwise fashion providing one of the many DESCRIPTION strategies that may lead to gene discovery. AUTHOR Skoufos, Emmanouil RT - ADDRESS Center for Medical Informatics ADDRESS and Section of Neurobiology ADDRESS Yale University School of Medicine ADDRESS 333 Cedar Street ADDRESS New Haven, CT 06511 CONTACT emmanouil.skoufos@yale.edu SITE WWW Server at URL http://www.geocities.com/CapeCanaveral/1915/gdp.html SITE-CONTACT - OS - LANGUAGE - VOLUME - REQUIRES - AC BC00552 NAME ESSA DOMAIN Sequence display DOMAIN Sequence analysis DOMAIN RNA analysis DOMAIN WWW server DESCRIPTION With ESSA, we propose an approach of RNA secondary DESCRIPTION structure analysis based on extensive viewing within a DESCRIPTION friendly graphical interface. This computer program is DESCRIPTION organized around the display of folding models produced by DESCRIPTION two complementary methods suitable to draw long RNA DESCRIPTION molecules. Any feature of interest can be managed directly DESCRIPTION on the display and highlighted by a rich combination of DESCRIPTION colours and symbols with emphasis given to structural probe DESCRIPTION accessibilities. ESSA also includes a word searching DESCRIPTION procedure allowing easy visual identification of structural DESCRIPTION features even complex and degenerated. Analysis functions DESCRIPTION make it possible to calculate the thermodynamic stability DESCRIPTION of any part of a folding using several models and compare DESCRIPTION homologous aligned RNA both in primary and secondary DESCRIPTION structure. The predictive capacities of ESSA which brings DESCRIPTION together the experimental, thermodynamic and comparative DESCRIPTION methods, are increased by coupling it with a program DESCRIPTION dedicated to RNA folding prediction based on constraints DESCRIPTION management AUTHOR Chetouani F., Monestie P., Thebault P., Gaspin C., Michot B. RA Chetouani F., Monestie P., Thebault P., Gaspin C., Michot B.; RT "ESSA: An integrated and interactive computer tool for RT analysing RNA secondary structure."; RL Nucleic Acids Res 25(17):3514-3522(1997). ADDRESS Gaspin : Station de Biometrie et d'Intelligence Artificielle, ADDRESS I.N.R.A., Chemin de Borde-Rouge, Auzeville BP 27, 31326 ADDRESS Castanet-Tolosan Cedex, FRANCE ADDRESS tel : (33) 05 61 28 52 82; fax : (33) 05 61 28 53 35; ADDRESS e-mail : gaspin@toulouse.inra.fr ADDRESS Michot, Chetouani ADDRESS Laboratoire de Biologie Moleculaire Eucaryote du C.N.R.S., ADDRESS Universite Paul Sabatier, 118 route de Narbonne, ADDRESS 31062 Toulouse Cedex, FRANCE ADDRESS tel : (33) 05 61 33 58 65; fax : (33) 05 61 33 58 86; ADDRESS e-mail : bmichot@ibcg.biotoul.fr farid@ibcg.biotoul.fr CONTACT essa@toulouse.inra.fr SITE WWW Server at URL http://www-bia.inra.fr/T/essa/Doc/essa_home.html OS UNIX : SUN, SGI, HP LANGUAGE C VOLUME 200 Kb REQUIRES - AC BC00556 NAME Webin DOMAIN Sequence data submissions DOMAIN WWW server SERVER http://www.ebi.ac.uk/submission/webin.html DESCRIPTION WebIn is the EBI's preferred tool for the submission of DESCRIPTION nucleotide sequence data anddescriptive information to DESCRIPTION the EMBL Nucleotide Sequence Database. AUTHOR Katarzyna Kruszewska RT - ADDRESS EMBL Outstation, European Boinformatics Institute ADDRESS Wellcome Trust Genome Campus ADDRESS Hinxton, Cambridge CB10 1SD, UK CONTACT datasub@ebi.ac.uk SITE WWW Server at URL http://www.ebi.ac.uk/embl/Submission/webin.html OS - LANGUAGE Perl, JavaScript VOLUME - REQUIRES - AC BC00560 NAME Alkami Expert for PCR DOMAIN Sequence analysis DOMAIN Genetic tools DOMAIN WWW server DOMAIN Statistical significance SERVER http://www.alkami.com DESCRIPTION A PCR (polymerase chain reaction)design, troubleshooting and DESCRIPTION optimization tool. Alkami PCR integrates PCR reference DESCRIPTION resources and statistical tools with a simple interface. AUTHOR - RT - ADDRESS Alkami Biosystems ADDRESS P.O. Box 11216 ADDRESS Berkeley, CA 94712-2216 CONTACT info@alkami.com SITE WWW Server at URL http://www.alkami.com OS - LANGUAGE - VOLUME - REQUIRES - COMMENTS This is a FREE online service intended to introduce COMMENTS molecular biologists to a powerful PCR optimization tool. AC BC00568 NAME JOY SERVER http://www-cryst.bioc.cam.ac.uk/cgi-bin/joy.cgi DOMAIN Protein sequence analysis DOMAIN Protein structure analysis DOMAIN Alignment editing and display DOMAIN WWW server DOMAIN Comparative analysis DESCRIPTION JOY is a program to annotate protein sequence alignments DESCRIPTION with three-dimensional (3D) structural features. It was DESCRIPTION developed to display 3D structural information in a sequence DESCRIPTION alignment and to help understand the conservation of amino DESCRIPTION acids in their specific local environments. The JOY DESCRIPTION representation now constitutes an essential part of the two DESCRIPTION databases of protein structure alignments: HOMSTRAD DESCRIPTION (http://www-cryst.bioc.cam.ac.uk/~homstrad) and CAMPASS DESCRIPTION (http://www-cryst.bioc.cam.ac.uk/~campass). It has also been DESCRIPTION successfully used for identifying distant evolutionary DESCRIPTION relationships. DESCRIPTION DESCRIPTION JOY takes an input alignment (or a single sequence) in a DESCRIPTION format similar to that of the NBRF/PIR format and produces a DESCRIPTION number of output files, including the annotated alignment in DESCRIPTION PostScript, LATEX and HTML. JOY requires a series of DESCRIPTION datafiles containing information about secondary structures, DESCRIPTION solvent accessibility and hydrogen bonding. These are DESCRIPTION produced automatically from a PDB file by supporting DESCRIPTION programs. AUTHOR Kenji Mizuguchi, Charlotte M. Deane, Tom L. Blundell, AUTHOR Mark S. Johnson, John P. Overington RA Mizuguchi K., Deane C.M., Johnson M.S., Blundell T.L., Overington J.P.; RT "JOY: protein sequence-structure representation and analysis."; RL Bioinformatics 14:617-623(1998). ADDRESS Department of Biochemistry ADDRESS University of Cambridge ADDRESS 80 Tennis Court Road ADDRESS Cambridge CB2 1GA ADDRESS UK CONTACT kenji@cryst.bioc.cam.ac.uk SITE WWW Server at URL http://www-cryst.bioc.cam.ac.uk/cgi-bin/joy.cgi OS UNIX LANGUAGE Fortran, C, Perl VOLUME - REQUIRES - COMMENTS Currently only executable files for IRIX5.3 or highter are COMMENTS available, but distribution of the source code to academic COMMENTS users will follow. AC NC00581 NAME SIMLYS DOMAIN Protein structure analysis DOMAIN WWW server SERVER http://bionm4.biochem.rwth-aachen.de/FB2/Simlys/simlys0.html DESCRIPTION SIMLYS a program for trajectory/conformational analysis of DESCRIPTION (bio)molecular simulations and/or experimental X-ray, NMR DESCRIPTION structures (PDB-format). Version 4.0 (1998) free available. DESCRIPTION Installation possible on various operating systems. AUTHOR Peter Krueger, Angelika Szameit RA Krueger, Lueke, Szameit; RL Comput.Phys.Commun. 62:371-380(1991). RA Krueger, Szameit; RL Comput.Phys.Commun. 72:265-268(1992). ADDRESS Peter Krueger ADDRESS Laboratory of Chemical and Biological Dynamics ADDRESS Katholieke Universiteit Leuven ADDRESS Celestijnenlaan 200 D ADDRESS B-3001 Leuven Belgium CONTACT E-mail: peter@lcbdiris.fys.kuleuven.ac.be CONTACT or : peter@bionm1.biochem.rwth-aachen.de SITE WWW Server at URL http://bionm4.biochem.rwth-aachen.de/FB2/Simlys/simlys0.html SITE-CONTACT - OS Unix, MS-Dos, Windos 95/NT LANGUAGE Fortran VOLUME 580 KB REQUIRES Fortran compiler 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 BC00583 NAME CloneIt Online DOMAIN Sequence tools DOMAIN Pattern Identification DOMAIN Restriction maps DOMAIN WWW server SERVER http://topaze.jouy.inra.fr DESCRIPTION Molecular biologists often have to sub-clone plasmidic DESCRIPTION vectors: a DNA plasmid is and ligated with an exogen DNA DESCRIPTION fragment previously excised from an other plasmid. The DESCRIPTION necessary cuts are achieved by restriction enzymes which DESCRIPTION then must be carefully choosen in order to minimize the DESCRIPTION steps required to obtain the desired molecule. During the DESCRIPTION selection of those enzymes, the main difficulties DESCRIPTION encountered come from: the knowldege of: DESCRIPTION the enzymes' characteristics DESCRIPTION the localization of the cuts within the sequence DESCRIPTION the complementarity between the protuding ends DESCRIPTION the possible self ligation of the vector DESCRIPTION the use of modifying DNA polymerases generating blunt ends DESCRIPTION the constraint to clone the insert in-frame with a vector sequence DESCRIPTION the use of partial digestions DESCRIPTION the creation of a stop codon after the ligation. DESCRIPTION We developed the CloneIt program that quickly finds DESCRIPTION in-frame deletions using restriction enzymes and DESCRIPTION frameshifts (using digestion, fill-in and ligation) in a DESCRIPTION plasmid sequence, Then, as the main functions and DESCRIPTION procedures were being developed, we have extended the DESCRIPTION capacities of the program to find strategies to sub-clone a DESCRIPTION fragment from a plasmid to another vector while still DESCRIPTION controling the problems described above. This program is DESCRIPTION not an expert system, as it does not "learn" the logical DESCRIPTION steps accomplished by the biologist and it does not have to DESCRIPTION be accompanied in its search: it just runs an algorithm DESCRIPTION that explores all the possible enzymes combinations that DESCRIPTION could be used to clone the molecules. DESCRIPTION This program provides a useful aid for any molecular DESCRIPTION biologist who wants to quickly find sub-cloning, in-frame DESCRIPTION deletions, frameshifts strategies, which would otherwise be DESCRIPTION difficult to discover. AUTHOR Pierre LINDENBAUM, Christophe CARON RA Lindenbaum P.; RT "CloneIt: finding cloning strategies, in-frame deletions and frameshifts."; RL Bioinformatics 14(5):465-466(1998). ADDRESS Pierre LINDENBAUM. ADDRESS Laboratoire de Biologie Moleculaire des Rotavirus. ADDRESS Virologie et Immunologie Moleculaires. ADDRESS Institut National de la Recherche Agronomique. ADDRESS 78350 Jouy-en-Josas Cedex FRANCE. ADDRESS lindenb@biotec.jouy.inra.fr CONTACT lindenb@biotec.jouy.inra.fr SITE WWW Server at URL http://topaze.jouy.inra.fr/cgi-bin/CloneIt/CloneIt OS - LANGUAGE - VOLUME - REQUIRES - COMMENTS Merci a Mademoiselle DERAT pour son aide. AC BC00600 NAME Jpred - consensus secondary structure prediction server DOMAIN Protein sequence analysis DOMAIN Protein structure analysis DOMAIN Structure prediction DOMAIN JAVA DOMAIN WWW server SERVER http://barton.ebi.ac.uk/servers/jpred.html DESCRIPTION Jpred is a internet web server that takes DESCRIPTION either a protein sequence or a mulitple alignment of DESCRIPTION protein sequences, and predicts secondary structure. It DESCRIPTION works by combining a number of modern, high quality DESCRIPTION prediction methods to form a consensus. DESCRIPTION DESCRIPTION Jpred runs DSC, PHD, PREDATOR and NNSSP to build it's consensus DESCRIPTION prediction, but predictions from older algorithms Mulpred and DESCRIPTION Zpred are also included in the final output. DESCRIPTION DESCRIPTION The consensus method has been shown, to be DESCRIPTION on average more accurate than any of the component methods, DESCRIPTION by ca. 1%. However the strength of this server lies in the DESCRIPTION fact that it leaves the final decision to the user who can DESCRIPTION use the supplied coloured HTML and Java viewer to decide DESCRIPTION where the best or most sensible consensus may be. AUTHOR Cuff J. A., Clamp M. E., Siddiqui A. S., Finlay M., Barton G. J. RA Cuff J. A. and Barton G. J.; RT "Evaluation and improvement of multiple sequence methods RT for protein secondary structure prediction."; RL PROTEINS: Structure, Function and Genetics. 34:508-519 (1999). RA Cuff, J. A., Clamp, M. E., Siddiqui, A. S., Finlay, M. RA and Barton, G. J. RT "Jpred: a consensus secondary structure prediction server."; RL Bioinformatics 14:892-893 (1998). ADDRESS EMBL-European BioInformatics Institute, ADDRESS Wellcome Trust Genome Campus, Hinxton Cambs. ADDRESS CB10 1SD, UK CONTACT geoff@ebi.ac.uk SITE WWW Server at URL http://barton.ebi.ac.uk/servers/jpred.html OS - LANGUAGE - VOLUME - REQUIRES Netscape/IE > 4, with JAVA AC BC00601 NAME Jalview DOMAIN Sequence display DOMAIN Sequence analysis DOMAIN Protein sequence analysis DOMAIN Alignment editing and display DOMAIN Alignment browser DOMAIN JAVA DOMAIN Multivariate analysis DOMAIN WWW server SERVER http://circinus.ebi.ac.uk:6543/jalview DESCRIPTION A multiple sequence alignment viewer and editor. Alignments DESCRIPTION can be divided into subfamilies using a tree or by hand. DESCRIPTION Conservation can then be calculated using physico-chemical DESCRIPTION properties within subfamilies or across the whole alignment. DESCRIPTION Principal component analysis can also be used as an DESCRIPTION alternative way of clustering the sequences. An SRS server DESCRIPTION can be used to fetch and display the sequence features and DESCRIPTION any PDB structures listed. There is limited access to DESCRIPTION external programs including clustalw and jnet secondary DESCRIPTION structure prediction. AUTHOR Michele Clamp RT - ADDRESS The Sanger Centre ADDRESS Wellcome Trust Genome Campus ADDRESS Hinxton ADDRESS Cambs. ADDRESS CB10 1SA ADDRESS UK CONTACT michele@sanger.ac.uk SITE WWW Server at URL http://circinus.ebi.ac.uk:6543/jalview OS - LANGUAGE java1.1 VOLUME 300kb REQUIRES Java runtime environment AC BC00602 NAME ProtEST Protein Multiple Sequence Alignments from ESTs DOMAIN Protein sequence analysis DOMAIN WWW server SERVER http://barton.ebi.ac.uk/servers/protest.html DESCRIPTION ProtEST Protein Multiple Sequence Alignments from ESTs DESCRIPTION ProtEST allows you to search an EST DESCRIPTION (expressed sequence tag) database with a protein. The DESCRIPTION significant hits are automatically checked and filtered DESCRIPTION before being aligned. DESCRIPTION ProtEST was written to solve the problem where you need a DESCRIPTION protein multiple sequence alignment e.g. for secondary DESCRIPTION structure prediction, and yet there are no sequences to be DESCRIPTION found in the current protein sequence database. AUTHOR Cuff J. A., E. Birney., M. E. Clamp, Barton G. J. RA Cuff J. A., E. Birney., M. E. Clamp, Barton G. J.; RT "ProtEST: Protein multiple sequence alignments from ESTs."; RL Bioinformatics: submited (1999) ADDRESS EMBL-European BioInformatics Institute, ADDRESS Wellcome Trust Genome Campus, Hinxton Cambs. ADDRESS CB10 1SD - UK CONTACT geoff@ebi.ac.uk SITE WWW Server at URL http://barton.ebi.ac.uk/servers/protest.html OS - LANGUAGE - VOLUME - REQUIRES Netscape/IE > 4, with JAVA .