Catalogue of Molecular Biology Programs Release 6.1 23 Jul 1999 All thanks are in the file biocatal.thanks. ===================================================================== AC BC00001 NAME ALIGN DOMAIN Alignment Search software DESCRIPTION Optimal global alignment of two sequences DESCRIPTION with no short-cuts. It will automatically decide DESCRIPTION whether the query sequence is DNA or protein by DESCRIPTION reading the query sequence as protein and DESCRIPTION determining whether the `amino-acid composition' DESCRIPTION is more than 85% A+C+G+T DESCRIPTION This program is a slightly modified version DESCRIPTION one taken from E. Myers and W. Miller. AUTHOR W.R. Pearson RA Pearson W.R., Lipman D.J.; RT "Improved Tools for Biological Sequence Comparison"; RL Proc. Natl. Acad. Sci. USA 85:2444-2448(1988). RX Medline; 88190088. RX SeqAnalRef; PEAW8201. RA Pearson W.R.; RT "Rapid and Sensitive Sequence Comparison with FASTP and FASTA"; RL Methods in Enzymology 183:63-98(1990). RX Medline; 9019039. RX SeqAnalRef; PEAW9001. RA Myers E., Miller W.; RT "Optimal Alignments in Linear Space"; RL Comput. Appl. Biosci. 4:11-17(1988). RX Medline; 88252871. RX SeqAnalRef; MYEE8801. ADDRESS U. of Virginia Dept. of Biochemistry, Charlottesville 22908,USA CONTACT W.R. Pearson: wrp@virginia.edu SITE ftp anonymous ftp.virginia.edu SITE Directory /pub/fasta SITE-CONTACT W.R. Pearson: wrp@virginia.edu OS Unix, VMS LANGUAGE C VOLUME - AC BC00002 NAME ALIGN - MBCRR DOMAIN Alignment Search software DESCRIPTION ALIGN is part of the MBCRR Software Package DESCRIPTION Optimally aligns a pair of sequences using the DESCRIPTION Needleman-Wunsch/Sellers *global* alignment DESCRIPTION algorithm. AUTHOR T. Smith RT - ADDRESS Molecular Biology Computer Research Resource ADDRESS Dana-Farber Cancer Institute and School of Public Health ADDRESS Harvard University, 44 Binney St., Boston MA 02115 USA. CONTACT Smith T: tsmith@mbcrr.harvard.edu SITE ftp anonymous mbcrr.harvard.edu SITE Directory /MBCRR-Package SITE-CONTACT Smith T: tsmith@mbcrr.harvard.edu OS Unix LANGUAGE C VOLUME - 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 BC00004 NAME AMPS DOMAIN Alignment Search software DESCRIPTION Multiple protein sequence alignment and flexible pattern DESCRIPTION matching programs. These do "normal" multiple alignment DESCRIPTION but also include features to make use of additional non DESCRIPTION sequence information (e.g. secondary structures) when DESCRIPTION this is available. AUTHOR Barton, G. J. (1993) RA Barton G.J.; RT "Protein Multiple Sequence Alignment and Flexible RT Pattern Matching"; RL Meth. Enzymol. 183:403-428(1990). RX Medline; 90190383. RX SeqAnalRef; BARG9002. RA Barton G.J., Sternberg M.J.E; RT "A Strategy for the Rapid Multiple Alignment of Protein RT sequences: Confidence Levels From Tertiary Structure RT Comparisons"; RL J. Mol. Biol. 198:327-337(1987). RX Medline; 88118932. RX SeqAnalRef; BARG8702. ADRESS University of Oxford Laboratory of Molecular Biophysics ADRESS Rex Richards Building , South Parks Road ADRESS Oxford OX1 3QU UK. CONTACT Barton, G. J.: gjb@bioch.ox.ac.uk SITE ftp anonymous geoff.biop.ox.ac.uk SITE Directory /programs/amps SITE Download the file README and Follow the instructions therein SITE-CONTACT Barton, G. J.: gjb@bioch.ox.ac.uk OS known to run on Sun and SGI, partial implementation under VMS). LANGUAGE Fortran 77 and C VOLUME - AC BC00005 NAME ASSET DOMAIN Alignment Search software DESCRIPTION Aligned Segment Statistical Evaluation Tool DESCRIPTION this programs does local multiple alignments DESCRIPTION by maximizing the log liklihood ratio statistic. AUTHOR A. F. Neuwald RA Neuwald A.F., Green P.; RT "Detecting patterns in protein sequences"; RL J. Mol. Biol. 239:698-712(1994). RX Medline; 94285214. RX SeqAnalRef; NEUA9401. ADDRESS National Center for Biotechnology Information ADDRESS National Library of Medicine, Bldg. 38A, Room 8N-811 ADDRESS Bethesda, MD 20894, USA. CONTACT neuwald@ncbi.nlm.nih.gov SITE ftp anonymous ncbi.nlm.nih.gov SITE Directory /pub/asset SITE-CONTACT - OS Unix (SunOS, SGI) LANGUAGE C VOLUME - REQUIRES - AC BC00006 NAME BANDS DOMAIN Alignment Search software DESCRIPTION package for aligning two sequences within DESCRIPTION a specified diagonal band. AUTHOR Chao, K.-M., Pearson, W.R. and Miller, W. RA Chao K.-M., Pearson W.R., Miller W.; RT "Aligning two sequences within a specified diagonal band."; RL Comput. Appl. Biosci. 8:481-487(1992). RX Medline; 93045596. RX SeqAnalRef; CHAK9201. ADDRESS (K-M Chao and W. Miller) ADDRESS Department of Computer Science and Engineering, ADDRESS The Pennsylvania State University, ADDRESS University Park, PA 16802, USA. ADDRESS (J. Zhang and J. Ostell) ADDRESS NCBI, NLM, NIH, Bethesda, MD 20894, USA. CONTACT webb@cse.psu.edu SITE ftp anonymous groucho.cs.psu.edu SITE Directory /band SITE-CONTACT - OS - LANGUAGE C VOLUME - AC BC00007 NAME BESTSCOR DOMAIN Alignment Search software DESCRIPTION Calculate the best self-comparison score. AUTHOR Pearson W.R. RT - ADDRESS U. of Virginia Dept. of Biochemistry, USA CONTACT wrp@virginia.edu SITE ftp anonymous ftp.virginia.edu SITE Directory /pub/fasta = fasta(version number) SITE-CONTACT W R Pearson: wrp@virginia.edu OS all LANGUAGE C VOLUME - AC BC00008 NAME BIOSCAN DOMAIN Alignment Search software DESCRIPTION BioSCAN (Biological Sequence Comparative DESCRIPTION Analysis Node) is a massively parallel DESCRIPTION computer system designed for biological DESCRIPTION sequence similarity analysis. This system DESCRIPTION performs rapid, rigorous, searches of DNA, DESCRIPTION RNA, and protein sequence databases and is DESCRIPTION compatible with popular software packages such DESCRIPTION as BLAST and FASTA. BioSCAN uses a rigorous DESCRIPTION implementation of linear similarity methods DESCRIPTION used in the BLAST systems. It is also well DESCRIPTION suited to multiscore applications using DESCRIPTION multiple PAM and BLOSUM scoring matrices. AUTHOR - RA White C.T., Singh R.K., Reintjes P.B., Lampe J., Erickson B.W., RA Dettloff W.D., Chi V.L., Altschul S.F.; RT "BioSCAN : A VLSI-Based System for Biosequence Analysis,"; RL 1991 IEEE International Conference on Computer Design: VLSI in RL Computers & Processors, IEEE Computer Society Press, Los RL Alamitos, CA, pp.504-509 (1991). RX SeqAnalRef; WHIC9101. RA Singh R.K., Tell S.G., White C.T., Hoffman D., Chi V.L., RA Erickson B.W.; RT "A scalable systolic multiprocessor system for analysis RT of biological sequences."; RL (In) Research on integrated systems. Proceedings of the RL 1993 symposium; RL Borriello G., Ebeling C., Eds., pp168-182, MIT Press, (1993). RX SeqAnalRef; SINK9301. ADDRESS NSF, under Grant No. MIP-9024585 ADDRESS MCNC, under Design Initiative Research Program CONTACT - SITE ftp anonymous ftp.cs.unc.edu SITE Directory /pub/bioscan SITE-CONTACT - OS Sun SPARC or DEC MIPS architecture workstation LANGUAGE - VOLUME - AC BC00009 NAME BLAST DOMAIN Alignment Search software DESCRIPTION Fast sequence database searching programs DESCRIPTION A new approach to rapid sequence comparison, DESCRIPTION basic local alignment search tool (BLAST), DESCRIPTION directly approximates alignments that optimize a DESCRIPTION measure of local similarity, the maximal segment DESCRIPTION pair (MSP) score. Recent mathematical results on DESCRIPTION the stochastic properties of MSP scores allow an DESCRIPTION analysis of the performance of this method as DESCRIPTION well as the statistical significance of DESCRIPTION alignments it generates. The basic algorithm is DESCRIPTION simple and robust; it can be implemented in a DESCRIPTION number of ways and applied in a variety of DESCRIPTION contexts including straightforward DNA and DESCRIPTION protein sequence database searches, motif DESCRIPTION searches, gene identification searches, and in DESCRIPTION the analysis of multiple regions of similarity in DESCRIPTION long DNA sequences. In addition to its DESCRIPTION flexibility and tractability to mathematical DESCRIPTION analysis, BLAST is an order of magnitude faster DESCRIPTION than existing sequence comparison tools of DESCRIPTION comparable sensitivity. AUTHOR NCBI, ported to VMS by Stockwell P. RA Altschul S.F., Gish W., Miller W., Myers E.W., Lipman D.J.; RT "Basic local alignment search tool."; RL J. Mol. Biol. 215:403-410(1990). RX Medline; 91039304. RX SeqAnalRef; ALTS9002. 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 SITE ftp anonymous ncbi.nlm.nih.gov SITE Directory /pub/blast SITE-CONTACT federhen@ncbi.nlm.nih.gov (S Federhen ) SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/unix/ UNIX software are stored SITE as archive (tar) files compressed (.Z). SITE-CONTACT nethelp@ebi.ac.uk SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/vax VAX software are stored as SITE uuencoded (.UUE) files. SITE-CONTACT nethelp@ebi.ac.uk SITE ftp anonymous ftp.bio.indiana.edu SITE Directory /molbio/search/blast UNIX software SITE are stored as archive (tar) files compressed (.Z) SITE-CONTACT Don Gilbert : gilbertd@cricket.bio.indiana.edu SITE ftp anonymous ftp.bchs.uh.edu (129.7.2.43)/ SITE Directory /pub/gene-server/unix SITE-CONTACT Dan Davison dbd@theory.bchs.uh.edu OS IBM Mainframe (AIX only) Sun-3, Sun-4, Silicon OS Graphics, Cray Y-MP UNICOS (all Unix OS Macintosh (A/UX only) LANGUAGE C VOLUME - REQUIRES Files DFA, GISH and NCBI are required! AC BC00010 NAME BLAST-SHELL DOMAIN Alignment Search software DOMAIN GCG tools DESCRIPTION These programs construct messages in the DESCRIPTION format expected by GenBank and send them by DESCRIPTION mail. The users do not have to be familiar DESCRIPTION with the format of the message that GenBank DESCRIPTION expects,nor with sending email across the DESCRIPTION network; however, they do need to know how to DESCRIPTION read the mail that GenBank returns. DESCRIPTION BLASTMAIL.COM initiates a BLAST search of one DESCRIPTION of the GenBank databases. DESCRIPTION BLASTMAILQ.COM sends a message to the GenBank DESCRIPTION BLAST server inquiring about the state of the DESCRIPTION queue. TOFASTA.FOR is a program that converts DESCRIPTION a GCG sequence to the Fasta format expected DESCRIPTION by the GenBank server. AUTHOR Stephen Clark RT - ADDRESS U. of Virginia Dept. of Biochemistry, USA CONTACT clark@galen.oci.utoronto.ca (Internet) SITE ftp anonymous ftp.bio.indiana.edu SITE Directory /molbio/vax SITE-CONTACT D Gilbert: gilbertd@cricket.bio.indiana.edu OS VAX/VMS LANGUAGE - VOLUME - REQUIRES This program will have to be compiled REQUIRES and linked under the GCG environment. AC BC00011 NAME BLAST3 DOMAIN Alignment Search software DESCRIPTION Basic Local Alignment Search Tool DESCRIPTION family of sequence database comparison DESCRIPTION programs blast3 compare an amino acid query DESCRIPTION sequence against a protein sequence database DESCRIPTION to identify statistically significant 3-way DESCRIPTION sequence alignments (the query sequence plus DESCRIPTION two database sequences) in which the component DESCRIPTION pairwise alignments are statistically DESCRIPTION insignificant. AUTHOR - RA Altschul S.F., Gish W., Miller W., Myers E.W., Lipman D.J.; RT "Basic local alignment search tool."; RL J. Mol. Biol. 215:403-410(1990). RX Medline; 91039304. RX SeqAnalRef; ALTS9002. 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 SITE ftp anonymous ncbi.nlm.nih.gov SITE Directory /pub/blast SITE-CONTACT federhen@ncbi.nlm.nih.gov SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/unix SITE-CONTACT nethelp@ebi.ac.uk OS all Unix LANGUAGE C VOLUME - REQUIRES Files DFA, GISH and NCBI are required! AC BC00012 NAME BLASTINC DOMAIN Alignment Search software DESCRIPTION Fast sequence database searching programs (C DESCRIPTION header files) See also BLASTVMS , BLASTLIB DESCRIPTION BLAST AUTHOR NCBI, ported to VMS by Stockwell P. RA Altschul S.F., Gish W., Miller W., Myers E.W., Lipman D.J.; RT "Basic local alignment search tool."; RL J. Mol. Biol. 215:403-410(1990). RX Medline; 91039304. RX SeqAnalRef; ALTS9002. ADDRESS National Center for Biotechnology Information ADDRESS National Library of Medicine, Bldg. 38A, Room 8N-811 ADDRESS Bethesda, MD 20894, USA. CONTACT - SITE ftp anonymous ncbi.nlm.nih.gov SITE Directory /pub/blast SITE-CONTACT federhen@ncbi.nlm.nih.gov (S Federhen ) SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/unix SITE-CONTACT nethelp@ebi.ac.uk 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 SITE ftp anonymous ftp.bio.indiana.edu SITE Directory /molbio/search/blast UNIX software SITE are stored as archive (tar) files compressed (.Z) SITE-CONTACT Don Gilbert : gilbertd@cricket.bio.indiana.edu OS IBM Mainframe (AIX only) Sun-3, Sun-4, Silicon OS Graphics, Cray Y-MP UNICOS (all Unix) OS Macintosh (A/UX only) LANGUAGE C VOLUME - REQUIRES Files DFA, GISH and NCBI are required! AC BC00013 NAME BLASTLIB DOMAIN Alignment Search software DESCRIPTION Fast sequence database searching programs DESCRIPTION (source code for C library functions). See DESCRIPTION also BLASTVMS , BLASTINC , BLAST AUTHOR NCBI, ported to VMS by Stockwell P. RA Altschul S.F., Gish W., Miller W., Myers E.W., Lipman D.J.; RT "Basic local alignment search tool."; RL J. Mol. Biol. 215:403-410(1990). RX Medline; 91039304. RX SeqAnalRef; ALTS9002. 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 SITE ftp anonymous ncbi.nlm.nih.gov SITE Directory /pub/blast SITE-CONTACT federhen@ncbi.nlm.nih.gov (S Federhen ) SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/unix SITE-CONTACT nethelp@ebi.ac.uk 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 SITE ftp anonymous ftp.bio.indiana.edu SITE Directory /molbio/search/blast UNIX software SITE are stored as archive (tar) files compressed (.Z) SITE-CONTACT Don Gilbert : gilbertd@cricket.bio.indiana.edu OS IBM Mainframe (AIX only) Sun-3, Sun-4, Silicon OS Graphics, Cray Y-MP UNICOS (all Unix) OS Macintosh (A/UX only) LANGUAGE C VOLUME - REQUIRES Files DFA, GISH and NCBI are required! AC BC00014 NAME BLASTN DOMAIN Alignment Search software DESCRIPTION Basic Local Alignment Search Tool DESCRIPTION family of sequence database comparison DESCRIPTION programs compare a nucleotide query sequence DESCRIPTION against a nucleotide sequence database. AUTHOR - RA Altschul S.F., Gish W., Miller W., Myers E.W., Lipman D.J.; RT "Basic local alignment search tool."; RL J. Mol. Biol. 215:403-410(1990). RX Medline; 91039304. RX SeqAnalRef; ALTS9002. 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 SITE ftp anonymous ncbi.nlm.nih.gov SITE Directory /pub/blast SITE-CONTACT federhen@ncbi.nlm.nih.gov (S Federhen ) SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/unix SITE-CONTACT nethelp@ebi.ac.uk SITE ftp anonymous ftp.bio.indiana.edu SITE Directory /molbio/search/blast UNIX software SITE are stored as archive (tar) files compressed (.Z) SITE-CONTACT Don Gilbert : gilbertd@cricket.bio.indiana.edu OS IBM Mainframe (AIX only) Sun-3, Sun-4, Silicon OS Graphics, Cray Y-MP UNICOS (all Unix) OS Macintosh (A/UX only) LANGUAGE C VOLUME - REQUIRES Files DFA, GISH and NCBI are required! AC BC00015 NAME BLASTP DOMAIN Alignment Search software DESCRIPTION Basic Local Alignment Search Tool DESCRIPTION family of sequence database comparison DESCRIPTION programs blastp: compare an amino acid DESCRIPTION query sequence against a protein sequence DESCRIPTION database. AUTHOR - RA Altschul S.F., Gish W., Miller W., Myers E.W., Lipman D.J.; RT "Basic local alignment search tool."; RL J. Mol. Biol. 215:403-410(1990). RX Medline; 91039304. RX SeqAnalRef; ALTS9002. 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 SITE ftp anonymous ncbi.nlm.nih.gov SITE Directory /pub/blast SITE-CONTACT federhen@ncbi.nlm.nih.gov (S Federhen ) SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/unix SITE-CONTACT nethelp@ebi.ac.uk SITE ftp anonymous ftp.bio.indiana.edu SITE Directory /molbio/search/blast UNIX software SITE are stored as archive (tar) files compressed (.Z) SITE-CONTACT Don Gilbert : gilbertd@cricket.bio.indiana.edu OS IBM Mainframe (AIX only) Sun-3, Sun-4, Silicon OS Graphics, Cray Y-MP UNICOS (all Unix) OS Macintosh (A/UX only) LANGUAGE C VOLUME - REQUIRES Files DFA, GISH and NCBI are required! AC BC00016 NAME BLASTVMS DOMAIN Alignment Search software DESCRIPTION Fast sequence database searching programs (VMS DESCRIPTION specific routines) See also BLAST , BLASTLIB DESCRIPTION BLASTINC AUTHOR NCBI, ported to VMS by Stockwell P. RA Altschul S.F., Gish W., Miller W., Myers E.W., Lipman D.J.; RT "Basic local alignment search tool."; RL J. Mol. Biol. 215:403-410(1990). RX Medline; 91039304. RX SeqAnalRef; ALTS9002. 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 VMS LANGUAGE - VOLUME - AC BC00017 NAME BLASTX DOMAIN Alignment Search software DESCRIPTION Basic Local Alignment Search Tool DESCRIPTION family of sequence database comparison DESCRIPTION programsblastx: compare a nucleotide DESCRIPTION query sequence translated in all 6 reading DESCRIPTION frames (3 on each strand) against a protein DESCRIPTION sequence database. AUTHOR - RA Altschul S.F., Gish W., Miller W., Myers E.W., Lipman D.J.; RT "Basic local alignment search tool."; RL J. Mol. Biol. 215:403-410(1990). RX Medline; 91039304. RX SeqAnalRef; ALTS9002. 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 SITE ftp anonymous ncbi.nlm.nih.gov SITE Directory /pub/blast SITE-CONTACT federhen@ncbi.nlm.nih.gov (S Federhen ) 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 CONTACT - OS - LANGUAGE - VOLUME - AC BC00018 NAME BLAST and FASTA scripts DOMAIN Alignment Search software DESCRIPTION Series of BLAST and FASTA scripts both for users and for Unix DESCRIPTION systems administrators who prepare BLAST indexes available via DESCRIPTION anonymous FTP. The database indexing scripts are specific for DESCRIPTION those who use the IntelliGenetics suite AUTHOR - RT - ADDRESS Department of Biochemistry, Stanford University, USA CONTACT - SITE ftp anonymous cmgm.stanford.edu (36.96.0.200) SITE Directory /pub/IGdb SITE-CONTACT Klinger: klingler@cmgm.stanford.edu OS - LANGUAGE - VOLUME - 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 BC00021 NAME INTERVALS & POINTS DOMAIN Alignment Search software DESCRIPTION Those two programs build gap-free multiple DESCRIPTION alignments ("blocks") from a family of pairwise alignments. DESCRIPTION INTERVALS does so by treating each alignment DESCRIPTION as a collection of "diagonal lines", DESCRIPTION while POINTS treats an alignment as a collection of DESCRIPTION points, i.e., pairs of matched sequence positions. DESCRIPTION The output of the two programs is, at least in theory, DESCRIPTION identical. In general, INTERVALS should run DESCRIPTION substantially faster and in much less space than DESCRIPTION POINTS. AUTHOR Miller Webb RA Miller W.; RT "Building multiple alignments from pairwise alignments."; RL Comput. Appl. Biosci. 9:169-176(1993). RX Medline; 93245045. RX SeqAnalRef; MILW9301. ADDRESS Department of Comupter Science, The Pennsylvania State University ADDRESS University Park, PA 16802, USA. CONTACT webb@cs.psu.edu SITE ftp anonymous groucho.cs.psu.edu SITE Directory /dist/blocks SITE-CONTACT - OS Unix LANGUAGE C VOLUME - AC BC00022 NAME BMB DOMAIN Alignment Search software DESCRIPTION These files contain programs for aligning two DESCRIPTION sequences within a specified region. AUTHOR Chao, K.-M., Hardison, R. C. and Miller, W. RA Chao K.-M., Hardison R.C., Miller W.; RT "Constrained sequence alignment"; RL Bull. Math. Biol. 55(3):503-524(1993). RX SeqAnalRef; CHAK9302. ADDRESS Dep. Computer Sci., Pennsylvania State Univ., University Park, ADDRESS PA 16802, USA CONTACT webb@cse.psu.edu SITE ftp anonymous groucho.cs.psu.edu SITE Directory /BMB SITE-CONTACT - OS Unix LANGUAGE C VOLUME - AC BC00023 NAME CLUSTAL V DOMAIN Alignment Search software DOMAIN Phylogeny DESCRIPTION Multiple sequence alignment AUTHOR Higgins D., Fuchs R. and Bleasby A.J. RA Higgins D.G., Bleasby A.J., Fuchs R.; RT "CLUSTAL V: improved software for multiple sequence alignment."; RL Comput. Appl. Biosci. 8:189-191(1992). RX Medline; 92274219. RX SeqAnalRef; HIGD9202. ADDRESS European Bioinformatics Institute ADDRESS Hinxton Hall, Hinxton, Cambridge CB10 1RQ, UK CONTACT Des.Higgins@ebi.ac.uk SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/unix UNIX software are stored SITE as archive (tar) files compressed (.Z). SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/vax VAX software are stored as SITE uuencoded (.UUE) files. SITE-CONTACT nethelp@ebi.ac.uk SITE ftp anonymous ftp.bio.indiana.edu SITE Directory /molbio/align SITE-CONTACT gilbertd@cricket.bio.indiana.edu SITE ftp anonymous ftp.bchs.uh.edu (129.7.2.43)/ SITE Directory /pub/gene-server/unix SITE-CONTACT Dan Davison dbd@theory.bchs.uh.edu OS Unix, Vax/VMS LANGUAGE C VOLUME - COMMENTS This software may be distributed and used COMMENTS freely, provided that you do not modify it COMMENTS without the permission of the authors. AC BC00024 NAME CLUSTAL W DOMAIN Alignment Search software DOMAIN Phylogeny DESCRIPTION Multiple sequence alignment. It is a complete overhaul and DESCRIPTION upgrade of CLUSTAL V DESCRIPTION From version 1.4, it is ported to MAC and PC : DESCRIPTION Thave a nice beefy machine. On a Power Mac or a Pentium box DESCRIPTION it is nice and fast. Two precompiled versions are supplied for Macs DESCRIPTION (Power mac and old mac versions). DESCRIPTION Mac: 1500 residues by 100 sequences DESCRIPTION Power Mac 3000 " " " " DESCRIPTION PC 1500 " " " " AUTHOR Higgins D., Thompson J., Gibson T. RA Thompson J.D., Higgins D.G., Gibson T.J.; RT "CLUSTAL W: improving the sensitivity of progressive RT multiple sequence alignment through sequence weighting, RT position-specific gap penalties and weight matrix choice."; RL Nucleic Acids Res. 22:4673-4680(1994). RX Medline; 95075648. RX SeqAnalRef; THOD9402. ADDRESS European Molecular Biology Laboratory ADDRESS Meyerhofstrasse 1, 69117 Heidelberg, Germany CONTACT Gibson@embl-heidelberg.de ADDRESS EMBL Outstation, Hinxton - The European Bioinformatics Institute ADDRESS Hinxton Hall, Hinxton, Cambridge CB10 1RQ, UK CONTACT Des.Higgins@ebi.ac.uk SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/unix/clustalw.tar.Z UNIX software are SITE stored as archive (tar) files compressed (.Z). SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/vax/clustalw.uue VAX software are SITE stored as uuencoded (.UUE) files. SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/mac/clustalw.sea.hqx (self extracting archive/binhex) SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/dos/clustal$.exe (self extracting ZIP archive) SITE-CONTACT nethelp@ebi.ac.uk SITE ftp anonymous ftp.bio.indiana.edu SITE Directory /molbio/align SITE-CONTACT gilbertd@cricket.bio.indiana.edu SITE ftp anonymous ftp.bchs.uh.edu (129.7.2.43)/ SITE Directory /pub/gene-server/unix SITE-CONTACT Dan Davison dbd@theory.bchs.uh.edu OS Vax/VMS, UNIX, MacOS, MS-DOS LANGUAGE C VOLUME - COMMENTS This software may be distributed and used COMMENTS freely, provided that you do not modify it COMMENTS without the permission of the authors. AC BC00025 NAME CONSENSUS DOMAIN Alignment Search software DESCRIPTION CONSENSUS, LCONSENSUS, WCONSENSUS DESCRIPTION These programs do multiple alignment by maximizing the DESCRIPTION information in the alignment matrix and generate some DESCRIPTION log-likelihood ratio statistics. "wconsensus" differs from the DESCRIPTION "consensus" program in that the user does not supply the widthhe DESCRIPTION pattern being sought. "lconsensus-gc" differs from the DESCRIPTION "wconsensus" program in that the alignments can contain DESCRIPTION insertions and deletions (i.e., indels). The performance of DESCRIPTION "lconsensus-gc" is still being tested. The "patser" program DESCRIPTION allows one to score the words of a sequence against a summary DESCRIPTION matrix obtained from the "consensus" or "wconsensus" program. DESCRIPTION The "gmat-inf-gc" program can do a crude graphing of the DESCRIPTION information content at each position of an alignment obtained DESCRIPTION with the "consensus", "wconsensus", or "lconsensus-gc" program. DESCRIPTION The "fasta-consensus" program converts a file from the FASTA DESCRIPTION sequence format to a sequence format that can be used by the DESCRIPTION "wconsensus" and "lconsensus-gc" programs. The input is from DESCRIPTION the standard input and the output is sent to the standard DESCRIPTION output. AUTHOR Gerald Hertz RT Stormo G.D., Hartzell G.W; RT "Identifying protein-binding sites from unaligned DNA fragments"; RL Proc. Natl. Acad. Sci. U.S.A 86:1183-1187(1989). RX Medline; 89145207. RA Hertz G.Z., Hartzell G.W., Stormo G.D.; RT "Identification of consensus patterns in unaligned DNA sequences RT known to be functionally related."; RL Comput. Appl. Biosci. 6:81-92(1990). RX Medline; 90298276. RX SeqAnalRef; HERG9001. ADDRESS Department of Molecular, Cellular, and Developmental Biology ADDRESS University of Colorado,Campus Box 347, Boulder CO 80309-0347,USA. ADDRESS tel : (1) (303) 492-1474 CONTACT hertz@boulder.colorado.edu SITE ftp anonymous beagle.colorado.edu SITE Directory /pub/Consensus SITE-CONTACT - OS Unix (MIPS, Dec, SGI, SunOS) LANGUAGE C VOLUME - REQUIRES - AC BC00026 NAME DARWIN DOMAIN Alignment Search software DESCRIPTION sequence analysis package DESCRIPTION such as PepPepSearch: search a protein DESCRIPTION sequence against the SWISS-PROT database DESCRIPTION using Smith-Waterman's version of dynamic DESCRIPTION programming. DESCRIPTION NuclPepSearch: search a nucleotide DESCRIPTION sequence directly against the entire SWISS- DESCRIPTION PROT database using the algorithm by Knecht DESCRIPTION and Gonnet. DESCRIPTION PepNuclSearch: search a protein sequence DESCRIPTION directly against the entire EMBL nucleotide DESCRIPTION database using the algorithm by Knecht and DESCRIPTION Gonnet MassSearch: search the SWISS-PROT DESCRIPTION database for sequences which when digested by DESCRIPTION the given enzyme will match the given set of DESCRIPTION weights. AUTHOR Knecht, Gonnet. RT - ADDRESS Computational Biochemistry Research Group ADDRESS (CBRG) ETH / Zurich / Switzerland CONTACT knecht@inf.ethz.ch SITE - SITE-CONTACT - OS - LANGUAGE - VOLUME - AC BC00027 NAME DASHER3 DOMAIN Alignment Search software DESCRIPTION MBCRR Software Package DESCRIPTION High-speed k-tuple/hash database search tool DESCRIPTION (uses a modified Lipman-Wilbur algorithm); DESCRIPTION designed to run **sets** of sequences against DESCRIPTION other sets; produces a list of the best matches DESCRIPTION using a Chi-square scoring statistic; does DESCRIPTION not perform alignments. AUTHOR T. Smith RT - ADDRESS Molecular Biology Computer Research Resource ADDRESS Dana-Farber Cancer Institute and School of Public Health ADDRESS Harvard University, 44 Binney St., Boston MA 02115 USA. CONTACT Smith T: tsmith@mbcrr.harvard.edu SITE ftp anonymous mbcrr.harvard.edu SITE Directory /MBCRR-Package SITE-CONTACT Smith T: tsmith@mbcrr.harvard.edu OS Unix LANGUAGE C VOLUME - AC BC00028 NAME DFBLAST DOMAIN Alignment Search software DESCRIPTION Module to read a BLAST output and to generate DESCRIPTION an annotated query. AUTHOR Jean Michel Claverie RA Claverie J.-M., States D.J.; RT "Information enhancement methods for large scale RT sequence analysis."; RT Comput. Chem. 17:191-201(1993). RX SeqAnalRef; CLAJ9302. ADDRESS National Center for Biotechnology Information ADDRESS National Library of Medicine, Bldg. 38A, Room 8N-811 ADDRESS Bethesda, MD 20894, USA. CONTACT jmc@ncbi.nlm.nih.gov SITE ftp anonymous ncbi.nlm.nih.gov SITE Directory /pub/jmc SITE-CONTACT federhen@ncbi.nlm.nih.gov (S Federhen ) OS C LANGUAGE C VOLUME - AC BC00029 NAME DTASK11S DOMAIN Alignment Search software DESCRIPTION Dtask is a program package for running unix DESCRIPTION workstations in parallel when comparing a DESCRIPTION protein- or DNA/RNA-sequence against a library DESCRIPTION of such sequences. AUTHOR Hauge G.E. RT - ADDRESS University of Oslo. Norway CONTACT - 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 OS SunOS 4.1.1 SUN 3/50, 3/60, 3/280, 3/480, OS 4/50, 4/75, 4/260,Sparc 10 ULTRIX 4.2A OS DEC 5000, DEC 3100.HP-UX HP710 OS IRIX 4.0.5 SGI-INDIGO LANGUAGE C VOLUME - AC BC00030 NAME DYNAMIC DOMAIN Alignment Search software DESCRIPTION MBCRR Software Package DESCRIPTION Will match one or more short sequences (each DESCRIPTION less than 200 bases) against a longer sequence DESCRIPTION (up to 200000 bases) using a fast dynamic DESCRIPTION programming algorithm; handles mismatches and DESCRIPTION gaps;produces a list of the sites of the DESCRIPTION best matches; does not generate alignments. DESCRIPTION At the MBCRR, we use DYNAMIC to searchsequences DESCRIPTION against David Ghosh's database of DNA DESCRIPTION regulatory sequence sites (the MBCRR does not DESCRIPTION re-distribute the Ghosh database; it can DESCRIPTION obtained the National Center for Biotechnology DESCRIPTION Information, National Library of Medicine via DESCRIPTION INTERNET anonymous ftp to ncbi.nlm.nih.gov . AUTHOR T. Smith RT - ADDRESS Molecular Biology Computer Research Resource ADDRESS Dana-Farber Cancer Institute and School of Public Health ADDRESS Harvard University, 44 Binney St., Boston MA 02115 USA. CONTACT Smith T: tsmith@mbcrr.harvard.edu SITE ftp anonymous mbcrr.harvard.edu SITE Directory /MBCRR-Package SITE-CONTACT tsmith@mbcrr.harvard.edu OS Unix LANGUAGE C VOLUME - AC BC00031 NAME FASTA DOMAIN Alignment Search software DESCRIPTION FASTA version 1.6 uses a new method for DESCRIPTION calculating optimal scores in a band (the DESCRIPTION optimization or last step in the FASTA DESCRIPTION algorithm). In addition, it uses a linear- DESCRIPTION space method for calculating the actual DESCRIPTION alignments. AUTHOR W R Pearson RA Pearson W.R., Lipman D.J.; RT "Improved Tools for Biological Sequence Analysis."; RL Proc. Natl. Acad. Sci. U.S.A 85:2444-2448(1988). RX Medline; 88190088. RX SeqAnalRef; PEAW8801. RA Pearson W.R.; RT "Rapid and Sensitive Sequence Comparison with FASTP and FASTA."; RL Meth. Enzymol. 183:63-98(1990). RX Medline; 90190399. RX SeqAnalRef; PEAW9001. ADDRESS U. of Virginia Dept. of Biochemistry, USA CONTACT W R Pearson: wrp@virginia.edu SITE ftp anonymous ftp.virginia.edu SITE Directory /pub/fasta SITE-CONTACT W. R. Pearson : wrp@virginia.edu SITE ftp anonymous ftp.bio.indiana.edu SITE Directory /molbio/search SITE gilbertd@cricket.bio.indiana.edu SITE-CONTACT D Gilbert : gilbertd@cricket.bio.indiana.edu OS all LANGUAGE - VOLUME - AC BC00032 NAME FASTEMBL DOMAIN Alignment Search software DESCRIPTION DCL shell for facilitating EMBL Mail-FASTA DESCRIPTION access AUTHOR Sonnhammer E. L. (Clark S.) RT - ADDRESS Sanger Centre, Hinxton Hall, Hinxton, Cambs CB10 1RQ, UK CONTACT esr@sanger.ac.uk 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 DCL VOLUME - COMMENTS The software is not maintained any more. AC BC00033 NAME FILTER DOMAIN Alignment Search software DESCRIPTION Set of programs for suboptimal alignments and DESCRIPTION recognition of reliably aligned regions in DESCRIPTION protein sequence comparisons and to multiply DESCRIPTION align and find conserved motifs from a set of DESCRIPTION sequences AUTHOR Argos, P., Vingron, M., Rechid, R. and McCaldon, P. RA Vingron M., Argos P.; RT "Determination of reliable regions in protein RT sequence alignments."; RL Protein Eng. 3:565-569(1990). RX Medline; 91017450. RX SeqAnalRef; VINM9001. RA Vingron M., Argos P.; RT "Motif recognition and alignment for many sequences by RT comparison of dot-matrices."; RL J. Mol. Biol. 218:33-43(1991). RX Medline; 91162649. RX SeqAnalRef; VINM9101. ADDRESS EMBL, Heildeberg, Germany CONTACT argos@embl-heidelberg.de SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/unix UNIX software are stored SITE as archive (tar) files compressed (.Z). SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/vax VAX software are stored as SITE uuencoded (.UUE) files. SITE-CONTACT nethelp@ebi.ac.uk SITE ftp anonymous ftp.bchs.uh.edu UNIX software SITE Directory /pub/gene-server/unix SITE ftp anonymous ftp.bchs.uh.edu VAX software SITE Directory /pub/gene-server/vms SITE-CONTACT Dan Davison : dbd@theory.bchs.uh.edu OS SUN 2,3 or 4 LANGUAGE FORTRAN C VOLUME - AC BC00034 NAME FSAP DOMAIN Alignment Search software DESCRIPTION Rapid Sequence Comparison DESCRIPTION The Fristensky Sequence Analysis Package (formerly Cornell DESCRIPTION Sequence Analysis Package) has proven to be a versatile, DESCRIPTION reliable, and highly portable suite of programs for sequence DESCRIPTION analysis. At the heart of the package is NUMSEQ, a sequence DESCRIPTION manipulation program that provides a large number of options for DESCRIPTION presentation of sequence data, as well as facilitating DESCRIPTION simulation of operations such as translation, subcloning and DESCRIPTION ligation. Restriction search programs predict fragments and ends DESCRIPTION from single or multiple, complete or parital digests. Rapid DESCRIPTION matrix similarity searches perform quantititive comparisons of DESCRIPTION nucleic acid and protein sequences. Programs for base/amino acid DESCRIPTION composition and ORF analysis are also provided. Programs are DESCRIPTION compatible with IUPAC-IUB ambiguity conventions, and can read a DESCRIPTION wide variety of sequence file formats. AUTHOR Brian Fristensky RT - ADDRESS Department of Plant Science, University of Manitoba, ADDRESS Winnipeg, MB R3T 2N2 CANADA CONTACT frist@ccu.umanitoba.ca SITE ftp anonymous ftp.cc.umanitoba.ca SITE Directory /psgendb SITE-CONTACT B Fristensky : frist@cc.umanitoba.ca SITE WWW Server at URL http://home.cc.umanitoba.ca/~psgendb/FSAP.html OS MS-DOS, SunOS , IBM/AIX, HP/UX. LANGUAGE C Pascal VOLUME - AC BC00035 NAME GAP DOMAIN Alignment Search software DESCRIPTION A Global Alignment Program DESCRIPTION The GAP program computes a global alignment of two sequences DESCRIPTION without penalizing terminal gaps. It delivers the alignment in DESCRIPTION linear space, so long sequences can be aligned. AUTHOR Xiaoqiu Huang RA Huang X.; RT "On global sequence alignment."; RL Comput. Appl. Biosci. 10:227-235(1994). RX SeqAnalRef; HUAX9402. RX Medline; 95007029. ADDRESS Xiaoqiu Huang Department of Computer Science ADDRESS Michigan Technological University Houghton, MI 49931, USA CONTACT huang@cs.mtu.edu SITE gopher Host: megasun.BCH.UMontreal.CA Port: 70 SITE URL gopher://megasun.BCH.UMontreal.CA:70/11/CMB/Phylogeny/Alignment/Gap SITE-CONTACT Tim Littlejohn tim@bch.umontreal.ca OS Unix systems on Sun workstations and under DOS systems on PCs. LANGUAGE C VOLUME - AC BC00036 NAME GENAL DOMAIN Alignment Search software DESCRIPTION Alignments of genomic sequences with coding DESCRIPTION regions AUTHOR Stoevlbaek J. RT - ADDRESS - CONTACT - 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 OS Unix LANGUAGE C VOLUME - AC BC00037 NAME GIBBS DOMAIN Alignment Search software DESCRIPTION Gibbs Sampling Strategy for Multiple Alignment DESCRIPTION An algorithm for finding multiple sites in multiple sequences AUTHOR - RA Lawrence C.E., Altschul S.F., Boguski M.S., Liu J.S., RA Neuwald A.F., Wootton J.C.; RT "Detecting Subtle Sequence Signals: A Gibbs Sampling RT Strategy for Multiple Alignment"; RL Science 262:208-214(1993). RX Medline; 94023958. RX SeqAnalRef; LAWE9301. 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 SITE ftp anonymous ncbi.nlm.nih.gov SITE Directory /pub/gibbs SITE-CONTACT federhen@ncbi.nlm.nih.gov OS - LANGUAGE The data structures used in this program are part of a package LANGUAGE of object oriented C code for molecular biological applications LANGUAGE developed by Andrew F. Neuwald. VOLUME - AC BC00038 NAME GenQuest DOMAIN Alignment Search software DESCRIPTION GenQuest (Q) is an integrated sequence comparison server which DESCRIPTION can be accessed via e-mail or through an X-based client. DESCRIPTION The purpose of the system is to allow rapid and sensitive DESCRIPTION comparison of DNA and protein sequence to existing DNA and DESCRIPTION protein sequence databases. The databases which can be accessed DESCRIPTION from the Q server include the Genome Sequence Database (GSDB) DESCRIPTION (daily updated DNA sequence database maintained at Los Alamos DESCRIPTION National Laboratory), Swissprot, Prosite, PDB(Protein Databank DESCRIPTION sequences of proteins with solved structures) and a database of DESCRIPTION human repetitive DNA sequences (from J. Jurka). The system uses DESCRIPTION a specialized parallel computing environment at Oak Ridge DESCRIPTION National Laboratory and is supported and curated by a number of DESCRIPTION groups in the Genome community. AUTHOR - RT - ADDRESS - CONTACT grailmail@ornl.gov SITE ftp anonymous arthur.epm.ornl.gov SITE Directory /pub/xgenQuest/sun SITE-CONTACT grailmail@ornl.gov SITE ftp anonymous arthur.epm.ornl.gov SITE Directory /pub/xgenQuest/dec SITE-CONTACT grailmail@ornl.gov OS Sparc stations running Open Windows 3.0 and Sun OS 4.1.3, or OS on Dec Alpha workstations running the OSF/1 operating system. OS Connection of the user's machine to the Internet is required. LANGUAGE - VOLUME - AC BC00039 NAME ISSC DOMAIN Alignment Search software DESCRIPTION Sensitive sequence comparison package DESCRIPTION including graphics program for visualisation DESCRIPTION and interaction with dotmatrices AUTHOR Argos,P.,Vingron,M.,Rechid, R.and McCaldon, P. RA Argos P.; RT "A sensitive procedure to compare amino acid sequences."; RL J. Mol. Biol. 193:385-396(1987). RX Medline; 87254215. RX SeqAnalRef; ARGP8701. RA Rechid R., Vingron M., Argos P.; RT "A new interactive protein sequence alignment program and RT comparison of its results with widely used algorithms."; RL Comput. Appl. Biosci. 5:107-113(1989). RX Medline; 89248597. RX SeqAnalRef; RECR8901. ADDRESS EMBL, Heidelberg, Germany CONTACT argos@embl-heidelberg.de SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/unix UNIX software are stored SITE as archive (tar) files compressed (.Z). SITE Directory /pub/software/vax VAX software are stored as SITE uuencoded (.UUE) files. SITE-CONTACT nethelp@ebi.ac.uk SITE ftp anonymous ftp.bchs.uh.edu (129.7.2.43)/ SITE Directory /pub/gene-server/unix SITE ftp anonymous ftp.bchs.uh.edu (129.7.2.43)/ SITE Directory /pub/gene-server/vms SITE-CONTACT Dan Davison: dbd@theory.bchs.uh.edu OS Dec LANGUAGE FORTRAN C UIS or DEC-Windows VOLUME - AC BC00040 NAME LALIGN DOMAIN Alignment Search software DESCRIPTION A rigorous local sequence alignment program DESCRIPTION that will display the N-best local alignments DESCRIPTION (N=10 by default). DESCRIPTION The LALIGN programs incorporate the DESCRIPTION "sim" algorithm described by Huang and Miller DESCRIPTION Adv. Appl. Math. 12:337-357(1991). AUTHOR - RT - ADDRESS U. of Virginia Dept. of Biochemistry CONTACT wrp@virginia.edu SITE ftp anonymous ftp.virginia.edu SITE Directory /pub/fasta = fasta(version number) SITE-CONTACT William Pearson wrp@virginia.edu OS all LANGUAGE - VOLUME - AC BC00041 NAME LAV DOMAIN Alignment Search software DESCRIPTION lav and related tools is an application that DESCRIPTION provides a way to display and browse through DESCRIPTION the sequence alignments computed by a variety DESCRIPTION of programs.(sim , blast ...) DESCRIPTION related tools : lat lav lax AUTHOR S. Schwartz, W. Miller, C.-M. Yang and R. AUTHOR Hardison, RA Schwartz S., Miller W., Yang C.-M., Hardison R.C; RT "Software tools for analyzing pairwise alignments RT of long sequences."; RL Nucleic Acids Res. 19:4663-4667(1991). RX Medline; 91367662. RX SeqAnalRef; SCHS9101. ADDRESS W. Miller ADDRESS Department of Computer Science and Engineering, ADDRESS The Pennsylvania State University, ADDRESS University Park, PA 16802, USA. CONTACT webb@cse.psu.edu SITE ftp anonymous groucho.cs.psu.edu SITE Directory /lav SITE-CONTACT - OS C LANGUAGE C VOLUME - AC BC00042 NAME LCP DOMAIN Alignment Search software DESCRIPTION Local Content Program DESCRIPTION A Program for Identifying Regions Satisfying a Content DESCRIPTION Requirement. The program takes a DNA sequence file, a file DESCRIPTION containing a content requirement, and a length cutoff (integer), DESCRIPTION and reports the regions of the sequence that satisfy the content DESCRIPTION requirement. AUTHOR Xiaoqiu Huang RA Huang X.; RT "An algorithm for identifying regions of a DNA sequence that RT satisfy a content requirement"; RL Comput. Appl. Biosci. 10:219-225(1994). RX SeqAnalRef; HUAX9401. ADDRESS Department of Computer Science ADDRESS Michigan Technological University Houghton, MI 49931, USA CONTACT Xiaoqiu Huang huang@cs.mtu.edu SITE gopher Host: megasun.BCH.UMontreal.CA Port:70 SITE URL gopher://megasun.BCH.UMontreal.CA:70/11/CMB/Phylogeny/Alignment/Lcp OS Sun LANGUAGE C VOLUME - AC BC00043 NAME LFASTA DOMAIN Alignment Search software DESCRIPTION local similarity searches showing local DESCRIPTION alignments.The algorithm used to calculate DESCRIPTION the local alignment in a band has been improved AUTHOR Chao, Pearson, and Miller RA Chao K.-M., Pearson W.R., Miller W; RT "Aligning two sequences within a specified diagonal band."; RL Comput. Appl. Biosci. 8:481-487(1992). RX Medline; 93045596. RX SeqAnalRef; CHAK9201. ADDRESS U. of Virginia Dept. of Biochemistry CONTACT wrp@virginia.edu SITE ftp anonymous ftp.virginia.edu SITE Directory /pub/fasta = fasta(version number) SITE-CONTACT William Pearson wrp@virginia.edu OS all LANGUAGE - VOLUME - AC BC00044 NAME LOCAL DOMAIN Alignment Search software DESCRIPTION MBCRR Software Package DESCRIPTION Optimally aligns a pair of sequences using DESCRIPTION the Smith-Waterman *local* alignment algorithm AUTHOR Smith T.F., Waterman M.S. RA Smith T.F., Waterman M.S.; RT "Identification of common molecular subsequences."; RL J. Mol. Biol. 147:195-197(1981). RX Medline; 81267385. RX SeqAnalRef; SMIT8102. ADDRESS Molecular Biology Computer Research Resource ADDRESS Dana-Farber Cancer Institute and School of Public Health ADDRESS Harvard University, 44 Binney St., Boston MA 02115 USA. CONTACT Smith T: tsmith@mbcrr.harvard.edu SITE ftp anonymous mbcrr.harvard.edu SITE Directory /MBCRR-Package SITE-CONTACT Smith T: tsmith@mbcrr.harvard.edu OS Unix LANGUAGE C VOLUME - AC BC00045 NAME MACAW DOMAIN Alignment Search software DOMAIN Alignment editing and display DESCRIPTION Multiple Alignment Construction & Analysis Workbench DESCRIPTION MACAW is a program for locating, analyzing, and editing blocks DESCRIPTION of localized sequence similarity among multiple seqences and DESCRIPTION linking them into a composite multiple alignment. AUTHOR Greg Schuler, Stephen Altschul RA Schuler G.D., Altschul S.F., Lipman D.J.; RT "A Workbench for Multiple Alignment Construction and Analysis."; RL Proteins 9:180-191(1991). RX Medline; 91172743. RX SeqAnalRef; SCHD9001. RA Lawrence C.E., Altschul S.F., Boguski M.S., Liu J.S., RA Neuwald A.F., Wootton J.C.; RT "Detecting Subtle Sequence Signals: A Gibbs Sampling RT Strategy for Multiple Alignment"; RL Science 262:208-214(1993). RX Medline; 94023958. RX SeqAnalRef; LAWE9301. RA Karlin S., Altschul S.F.; RT "Methods for assessing the statistical significance of molecular RT sequence features by using general scoring schemes."; RL Proc. Natl. Acad. Sci. U.S.A. 87:2264-2268(1990). RX Medline; 90192788. RX SeqAnalRef; KARS9001. ADDRESS National Center for Biotechnology Information ADDRESS National Library of Medicine, Bldg. 38A, Room 8N-811 ADDRESS Bethesda, MD 20894, USA. CONTACT schuler@ncbi.nlm.nih.gov, altschul@ncbi.nlm.nih.gov SITE ftp anonymous ncbi.nlm.nih.gov SITE Directory /pub/macaw SITE-CONTACT - SITE WWW Server at URL http://www.ncbi.nlm.nih.gov OS PC (Windows 3.1x) WindowsNT, MAC(680x0) LANGUAGE - VOLUME - REQUIRES - AC BC00046 NAME MALI and PRALI DOMAIN Alignment Search software DESCRIPTION These programs are based on the algorithm DESCRIPTION described in:Martin Vingron and Patrick Argos DESCRIPTION A fast and sensitive multiple sequence DESCRIPTION alignment algorithm. AUTHOR Martin Vingron RA Vingron M., Argos P.; RT "A fast and sensitive multiple sequence alignment algorithm."; RT Comput. Appl. Biosci. 5(2):115-121(1989). RX Medline; 89248598. RX SeqAnalRef; VINM8901. ADDRESS EMBL, Heidelberg, Germany CONTACT Martin Vingron vingron@embl-heidelberg.de OS Sun-3, Unix Sun-4, Unix VAX, Unix LANGUAGE - VOLUME - COMMENTS The software will not be distributed to others COMMENTS beyond the immediate research group without COMMENTS the permission of the authors. AC BC00047 NAME MAP DOMAIN Alignment Search software DESCRIPTION The MAP program computes a multiple global alignment of sequences DESCRIPTION using iterative pairwise method. The underlying algorithm for DESCRIPTION aligning two sequences computes a best overlapping alignment DESCRIPTION between two sequences without penalizing terminal gaps. The MAP DESCRIPTION is designed in a space-efficient manner, so long sequences can be DESCRIPTION aligned. AUTHOR Xiaoqiu Huang RA Huang X.; RT "On global sequence alignment."; RL Comput. Appl. Biosci. 10:227-235(1994). RX SeqAnalRef; HUAX9402. RX Medline; 95007029. ADDRESS Xiaoqiu Huang Department of Computer Science ADDRESS Michigan Technological University Houghton, MI 49931, USA CONTACT Xiaoqiu Huang huang@cs.mtu.edu SITE gopher Host: megasun.BCH.UMontreal.CA Port:70 SITE URL gopher://megasun.BCH.UMontreal.CA:70/11/CMB/Phylogeny/Alignment/Map OS Unix systems on Sun workstations LANGUAGE C VOLUME - AC BC00048 NAME MBLKP and MBLKN DOMAIN Alignment Search software DESCRIPTION Utilities for Finding Local Multiple Similarities DESCRIPTION Two utilities are provided to perform a search for DESCRIPTION blocks of local similarity along multiple protein (mblkp) DESCRIPTION and nucleic acid (mblkn) sequences using the MACAW search DESCRIPTION algorithm (Schuler, et al., 1991). Unlike MACAW, which requires DESCRIPTION Microsoft Windows graphical interface, these simple DESCRIPTION utilities are designed as console-style programs, DESCRIPTION and as such, may be compiled for execution on a wide DESCRIPTION variety of platform. DESCRIPTION Note that without a graphical interface, much of the DESCRIPTION functionality of the MACAW program cannot be included. DESCRIPTION In particular, it is not possible to link the blocks DESCRIPTION together to form a composite multiple alignment. AUTHOR Greg Schuler RA Schuler G.D., Altschul S.F., Lipman D.J.; RT "A Workbench for Multiple Alignment Construction and Analysis."; RL Proteins 9:180-191(1991). RX Medline; 91172743. RX SeqAnalRef; SCHD9001. RA Karlin S., Altschul S.F.; RT "Methods for assessing the statistical significance of molecular RT sequence features by using general scoring schemes."; RL Proc. Natl. Acad. Sci. U.S.A. 87:2264-2268(1990). RX Medline; 90192788. RX SeqAnalRef; KARS9001. ADDRESS National Center for Biotechnology Information ADDRESS National Library of Medicine, Bldg. 38A, Room 8N-811 ADDRESS Bethesda, MD 20894, USA. CONTACT schuler@ncbi.nlm.nih.gov SITE ftp anonymous ncbi.nlm.nih.gov SITE Directory /pub/macaw/.misc/demosrc SITE-CONTACT - SITE WWW Server at URL http://www.ncbi.nlm.nih.gov OS SunOS 4.1.1, UNICOS 6.1.5 (CrayYMP), PC (MS-DOS 3.x, 5.0) LANGUAGE C VOLUME - REQUIRES - AC BC00049 NAME MEMFILE DOMAIN Alignment Search software DESCRIPTION Memfile is part of blast package DESCRIPTION Basic Local Alignment Search Tool DESCRIPTION family of sequence database comparison DESCRIPTION programs manage the loading, updating, and DESCRIPTION dropping of files mapped into shared memory DESCRIPTION segments. AUTHOR - RT - 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 SITE ftp anonymous ncbi.nlm.nih.gov SITE Directory /pub/blast SITE-CONTACT federhen@ncbi.nlm.nih.gov (S Federhen ) OS - LANGUAGE C VOLUME - AC BC00050 NAME MOTIF DOMAIN Alignment Search software DESCRIPTION Motif searching program AUTHOR Giles I. RA Cockwell K.Y., Giles I.G.; RT "Software tools for motif and pattern scanning: program RT descriptions including a universal sequence reading algorithm."; RL Comput. Appl. Biosci. 5:227-232(1989). RX Medline; 89353669. RX SeqAnalRef; COCK8901. 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 SITE ftp anonymous ftp.bchs.uh.edu (129.7.2.43)/ SITE Directory /pub/gene-server/vms SITE-CONTACT Dan Davison: dbd@theory.bchs.uh.edu OS Vax/VMS 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 BC00053 NAME PIMA DOMAIN Alignment Search software DESCRIPTION Pattern-induced multi-sequence alignment DESCRIPTION program AUTHOR Smith, R.F. and Smith T.F. RA Smith R.F., Smith T.S.; RT "Automatic generation of primary sequence patterns from sets RT of related protein sequences."; RL Proc. Natl. Acad. Sci. U.S.A. 87:118-122(1990). RX Medline; 90115821. RX SeqAnalRef; SMIR9001. RA Smith R.F., Smith T.S.; RT "Pattern-induced multi-sequence alignment (PIMA) algorithm RT employing secondary structure-dependent gap penalties for RT comparitive protein modelling."; RL Protein Eng. 5:35-41 (1992). RX Medline; 92335156. ADDRESS Temple Smith ADDRESS Molecular Bio-Enginnering Research Center ADDRESS Boston Univ., 36 Cummington St, Boston, MA 02115, USA CONTACT Temple Smith : tsmith@tsmith@darwin.bu.edu ADDRESS Brent Wiese and Randall Smith ADDRESS Human Genome Center ADDRESS Department of Molecular and Human Genetics ADDRESS Baylor College of Medicine, Houston, TX 77030 USA CONTACT Brent Wiese and Randall Smith : {brent,rsmith}@bcm.tmc.edu SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/unix UNIX software are stored SITE as archive (tar) files compressed (.Z). SITE-CONTACT nethelp@ebi.ac.uk SITE ftp anonymous mbcrr.harvard.edu SITE Directory /MBCRR-Package SITE-CONTACT tsmith@darwin.bu.edu SITE ftp anonymous gc.bcm.tmc.edu SITE Directory /pub/software/pima SITE WWW Server at URL http://dot.imgen.bcm.tmc.edu:9331/multi-align/multi-align.html SITE-CONTACT rsmith@bcm.tmc.edu SITE ftp anonymous ftp.bio.indiana.edu SITE Directory /molbio/unix SITE-CONTACT Don Gilbert: gilbertd@cricket.bio.indiana.edu SITE ftp anonymous ftp.bchs.uh.edu (129.7.2.43)/ SITE Directory /pub/gene-server/unix SITE-CONTACT Dan Davison: dbd@theory.bchs.uh.edu OS Unix LANGUAGE C VOLUME - COMMENTS The PIMA package is available free of charge COMMENTS to non-profit organizations; a distribution COMMENTS fee and non-resale agreement is required COMMENTS for commercial use. AC BC00054 NAME PLALIGN DOMAIN Alignment Search software DESCRIPTION a version of lalign that plots the local DESCRIPTION alignments to a screen or to a Tektronix DESCRIPTION terminal emulator. DESCRIPTION The PLALIGN program incorporate the de "sim" DESCRIPTION algorithm described by Huang and Miller DESCRIPTION Adv. Appl. Math. 12:337-357(1991). AUTHOR William Pearson RT - ADDRESS U. of Virginia Dept. of Biochemistry CONTACT wrp@virginia.edu SITE ftp anonymous ftp.virginia.edu SITE Directory /pub/fasta = fasta(version number) SITE-CONTACT William Pearson wrp@virginia.edu OS all LANGUAGE - VOLUME - AC BC00055 NAME PLFASTA - PCLFASTA DOMAIN Alignment Search software DESCRIPTION PLFASTA : local similarity searches with plot DESCRIPTION output (on the IBM, this program requires DESCRIPTION that the environment variable BGIDIR be DESCRIPTION set).PCLFASTA(unix only) local similarity DESCRIPTION searches with plot output using pic commands. AUTHOR William Pearson RT - ADDRESS U. of Virginia Dept. of Biochemistry CONTACT wrp@virginia.edu SITE ftp anonymous ftp.virginia.edu SITE Directory /pub/fasta = fasta(version number) SITE-CONTACT William Pearson wrp@virginia.edu OS all LANGUAGE - VOLUME - AC BC00056 NAME PLSEARCH DOMAIN Alignment Search software DOMAIN Pattern Identification DESCRIPTION A database of primary sequence patterns, DESCRIPTION constructed from all sequence families in DESCRIPTION EMBL's SWISS-PROT protein sequence database, DESCRIPTION and a dynamic-programming search tool for DESCRIPTION matching newly-generated sequences against DESCRIPTION the pattern library AUTHOR Smith, R.F. and Smith T.F. RA Smith R.F., Smith T.S.; RT "Automatic generation of primary sequence patterns from sets RT of related protein sequences."; RL Proc. Natl. Acad. Sci. U.S.A. 87:118-122(1990). RX Medline; 90115821. RX SeqAnalRef; SMIR9001. ADDRESS Molecular Biology Computer Research Resource ADDRESS Dana-Farber Cancer Institute and School of Public Health ADDRESS Harvard University, 44 Binney St., Boston MA 02115 USA. CONTACT Smith T: tsmith@mbcrr.harvard.edu SITE ftp anonymous mbcrr.harvard.edu SITE Directory /MBCRR-Package SITE-CONTACT Smith T: tsmith@mbcrr.harvard.edu SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/unix UNIX software are stored SITE as archive (tar) files compressed (.Z). SITE-CONTACT nethelp@ebi.ac.uk SITE ftp anonymous ftp.bchs.uh.edu SITE Directory /pub/gene-server/unix SITE-CONTACT Dan Davison: dbd@theory.bchs.uh.edu OS Unix LANGUAGE C VOLUME - AC BC00057 NAME PRDF DOMAIN Alignment Search software DESCRIPTION a version of RDF2 that uses calculates the probability of a DESCRIPTION similarity score more accurately by using a fit to an extreme DESCRIPTION value distribution. Code to fit the extreme value distribution DESCRIPTION parameters and the impetus to update RDF2 was provided by Phil DESCRIPTION Green, Washington U., St.Louis. AUTHOR - ADDRESS U. of Virginia Dept. of Biochemistry CONTACT wrp@virginia.edu SITE ftp anonymous ftp.virginia.edu SITE Directory /pub/fasta = fasta(version number) SITE-CONTACT William Pearson wrp@virginia.edu OS all LANGUAGE - VOLUME - AC BC00058 NAME PRESSDB DOMAIN Alignment Search software DESCRIPTION Basic Local Alignment Search Tool DESCRIPTION family of sequence database comparison DESCRIPTION programs produce a nucleotide sequence DESCRIPTION database for use by blastn and tblastn from a DESCRIPTION multi-sequence file in FASTA format. AUTHOR - RT - 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 SITE ftp anonymous ncbi.nlm.nih.gov SITE Directory /pub/blast SITE-CONTACT federhen@ncbi.nlm.nih.gov OS - LANGUAGE - VOLUME - AC BC00059 NAME PRSS DOMAIN Alignment Search software DESCRIPTION a version of PRDF that uses a rigorous Smith-Waterman DESCRIPTION calculation to score similarities AUTHOR William Pearson ADDRESS U. of Virginia Dept. of Biochemistry CONTACT wrp@virginia.edu SITE ftp anonymous ftp.virginia.edu SITE Directory /pub/fasta = fasta(version number) SITE-CONTACT William Pearson wrp@virginia.edu OS all LANGUAGE - VOLUME - AC BC00060 NAME PYTHIA DOMAIN Alignment Search software DESCRIPTION Allows the identification of human repetitive DESCRIPTION DNA elements such as L1, MERx, LTR, etc. Can DESCRIPTION also be used to identify the presence of Alu DESCRIPTION sequences and to classify them into sub- DESCRIPTION families. RT - ADDRESS Argonne National Laboratory, Argonne, Illinois, USA. CONTACT - SITE ftp everest.bim.anl.gov SITE Directory /pub SITE_CONTACT operator@everest.bim.anl.gov OS SunOS.4.1.2 on SUN Sparcstation 2 LANGUAGE UNIX C-shell scripts VOLUME - AC BC00061 NAME ROBUST DOMAIN Alignment Search software DESCRIPTION locating well-conserved regions within a DESCRIPTION pairwise alignment. AUTHOR Chao, K.-M., Hardison, R. C. and Miller, W. RA Chao K.-M., Hardison R.C., Miller W.; RT "Locating well-conserved regions within a pairwise alignment."; RL Comput. Appl. Biosci. 9:387-396(1993). RX Medline; 94005756. RX SeqAnalRef; CHAK9301. ADDRESS - CONTACT - SITE ftp anonymous groucho.cs.psu.edu SITE Directory /pub/dist/robust SITE-CONTACT - OS - LANGUAGE C VOLUME - AC BC00062 NAME RSS DOMAIN Alignment Search software DESCRIPTION a version of RDF2 that uses a rigorous Smith- DESCRIPTION Waterman calculation to score similarities DESCRIPTION The RSS program incorporate algorithms DESCRIPTION described by Huang, Hardison, and Miller DESCRIPTION Comput. Appl. Biosci. 6:373-381(1990). AUTHOR - RT - ADDRESS U. of Virginia Dept. of Biochemistry CONTACT wrp@virginia.edu SITE ftp anonymous ftp.virginia.edu SITE Directory /pub/fasta = fasta(versionnumber) SITE-CONTACT William Pearson wrp@virginia.edu OS all LANGUAGE - VOLUME - AC BC00063 NAME RTHEORY DOMAIN Alignment Search software DESCRIPTION This is a hidden Markov model nucleic acid alignment tool with a DESCRIPTION statistical test (likelihood ratio) for relatedness. DESCRIPTION Alignment of 2-strings under 1, 3 and 5-state models DESCRIPTION & estimation of evolutionary "distance" DESCRIPTION by optimal alignment and also `r-theory'. AUTHOR Lloyd ALLISON RA Allison L., Wallace C.S., Yee C.N.; RT "Finite-state models in the alignment of macromolecules."; RL J. Mol. Evol. 35:77-89(1992). RX Medline; 92389370. RX SeqAnalRef; ALLL9201. RA Yee C.N., Allison L.; RT "Reconstruction of strings past."; RL Comp. Appl. Biosci. 9(1):1-7(1993). RX Medline; 93169488. RX SeqAnalRef; YEEC9301. ADDRESS Dept. of Computer Science, Monash University, ADDRESS Clayton, Victoria 3168, AUSTRALIA ADDRESS tel: 61 3 905 5205 fax: 61 3 905 5146 CONTACT lloyd@cs.monash.edu.au SITE ftp anonymous bruce.cs.monash.edu.au SITE Directory /pub/lloyd/Alignment SITE-CONTACT lloyd@cs.monash.edu.au OS Unix LANGUAGE C VOLUME - REQUIRES - AC BC00064 NAME SETDB DOMAIN Alignment Search software DESCRIPTION Basic Local Alignment Search Tool DESCRIPTION family of sequence database comparison DESCRIPTION programs produce a protein sequence database DESCRIPTION for use by blastp, blastx,and blast3 from a DESCRIPTION multi-sequence file in FASTA format. AUTHOR - RT - 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 SITE ftp anonymous ncbi.nlm.nih.gov SITE Directory /pub/blast SITE-CONTACT federhen@ncbi.nlm.nih.gov OS - LANGUAGE - VOLUME - AC BC00065 NAME SIM DOMAIN Alignment Search software DESCRIPTION Local similarity program for use with the LAD/ DESCRIPTION LAV interface. AUTHOR Huang G. and Miller W. RA Huang X., Hardison R.C., Miller W.; RT "A space-efficient algorithm for local similarities."; RL Comput. Appl. Biosci. 6:373-381(1990). RX Medline; 91077763. RX SeqAnalRef; HUAX9001. ADDRESS Department of Computer Science and Engineering, ADDRESS The Pennsylvania State University, ADDRESS University Park, PA 16802, USA. CONTACT webb@cse.psu.edu SITE ftp anonymous groucho.cs.psu.edu SITE Directory /sim SITE-CONTACT - SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/vax VAX software are stored as SITE uuencoded (.UUE) files. SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/unix UNIX software are stored SITE as archive (tar) files compressed (.Z). SITE-CONTACT nethelp@ebi.ac.uk SITE ftp anonymous ftp.bchs.uh.edu (129.7.2.43)/ SITE Directory /pub/gene-server/unix SITE ftp anonymous ftp.bchs.uh.edu (129.7.2.43)/ SITE Directory /pub/gene-server/vms SITE-CONTACT Dan Davison: dbd@theory.bchs.uh.edu OS Unix Vax/VMS LANGUAGE C VOLUME - AC BC00066 NAME SIMPLE34 DOMAIN Alignment Search software DESCRIPTION SIMPLE34 extends and makes more widely available the SIMPLE DESCRIPTION program originally described by Tautz, Trick & Dover DESCRIPTION (Nature 322:652-656(1986)). DESCRIPTION The aim of the program is to estimate the level of local DESCRIPTION sequence repetition in nucleotide sequences. It does this DESCRIPTION by analysing the degree of clustering of short sequence DESCRIPTION motifs (3- and 4-mers). A significant level of clustering of DESCRIPTION short motifs has been suggested to reflect the action of DESCRIPTION replication slippage in the recent evolutionary history of DESCRIPTION sequences and is associated with length polymorphism in a DESCRIPTION variety of sequences including ribosomal RNAs, the mitochondrial DESCRIPTION control region and the transcription factor TBP. AUTHOR John Hancock RA Hancock J.M., Armstrong J.S.; RT "SIMPLE34: an improved and enhanced implementation for VAX RT and Sun computers of the SIMPLE algorithm for analysis of RT clustered repetitive motifs in nucleotide sequences."; RL Comput. Appl. Biosci. 10:67-70(1994). RX Medline; 94251650. RX SeqAnalRef; HANJ9401. ADDRESS Research School of Biological Sciences ADDRESS Australian National University,Canberra, ACT 0200, Australia. CONTACT John.Hancock@anu.edu.au SITE ftp anonymous life.anu.edu.au SITE Directory: /pub/molecular_biology/software/simple34 SITE Subdirectories /vax and /sun contain the directories simple34. SITE gopher Host: life.anu.edu.au Port: 70 SITE URL gopher://life.anu.edu.au:70/11/molecular_biology/software/simple OS Vax and Sun platforms. LANGUAGE FORTRAN77 VOLUME - AC BC00067 NAME SP2FASTA DOMAIN Alignment Search software DESCRIPTION Basic Local Alignment Search Tool DESCRIPTION family of sequence database comparison DESCRIPTION programs produce a file in FASTA format DESCRIPTION from one in SWISSPROT(R) or EMBL flat DESCRIPTION file format. AUTHOR - RT - 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 SITE ftp anonymous ncbi.nlm.nih.gov SITE Directory /pub/blast SITE-CONTACT federhen@ncbi.nlm.nih.gov OS - LANGUAGE - VOLUME - AC BC00068 NAME SSEARCH DOMAIN Alignment Search software DESCRIPTION a program to search a sequence database DESCRIPTION using the rigorous Smith-Waterman algorithm DESCRIPTION (this program is about 100-fold slower than DESCRIPTION FASTA with ktup=2 (for proteins). DESCRIPTION The SSEARCH program incorporate algorithms DESCRIPTION described by Huang, Hardison, and Miller DESCRIPTION Comput. Appl. Biosci. 6:373-381(1990). AUTHOR - RT - ADDRESS - CONTACT - SITE ftp anonymous virginia.edu SITE Directory /pub/fasta/fasta17 SITE-CONTACT - OS - LANGUAGE - VOLUME - AC BC00069 NAME STAMP DOMAIN Alignment Search software DESCRIPTION Alignment of multiple protein structures. Database scanning DESCRIPTION with a 3D structure. NOTE this package deals with 3D structures DESCRIPTION NOT sequences, but a sequence alignment is one result AUTHOR Russell R.B., Barton G.J. RA Russell R.B., Barton G.J.; RT "Multiple protein sequence alignment from tertiary structure RT comparison: assignment of global and residue confidence levels"; RL Proteins 14:309-323(1992). RX Medline; 93028364. RX SeqAnalRef; RUSR9201. RA Russell R.B., Barton G.J.; RT "An SH2-SH3 domain hybrid."; RL Nature 364:765(1993). RX Medline; 93361140. ADRESS University of Oxford Laboratory of Molecular Biophysics ADRESS Rex Richards Building , South Parks Road ADRESS Oxford OX1 3QU UK. CONTACT Barton, G. J. gjb@bioch.ox.ac.uk SITE ftp anonymous geoff.biop.ox.ac.uk SITE Directory / SITE Download the file README and Follow the instructions therein SITE-CONTACT gjb@bioch.ox.ac.uk SITE WWW server at URL http://geoff.biop.ox.ac.uk/ SITE-CONTACT gjb@bioch.ox.ac.uk OS Sun, SGI LANGUAGE C and fortran VOLUME - AC BC00070 NAME TBLASTN DOMAIN Alignment Search software DESCRIPTION Basic Local Alignment Search Tool DESCRIPTION family of sequence database comparison DESCRIPTION programs tblastn: compare an amino acid query DESCRIPTION sequence against a nucleotide sequence DESCRIPTION database translated in all 6 reading frames. AUTHOR - RT - 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 SITE ftp anonymous ncbi.nlm.nih.gov SITE Directory /blast SITE-CONTACT federhen@ncbi.nlm.nih.gov OS - LANGUAGE C VOLUME - AC BC00071 NAME TDALIGN DOMAIN Alignment Search software DESCRIPTION - AUTHOR Dan Davison and Keith Thompsom RA Davison D.B., Thompson K.H.; RT "A non-metric sequence alignment algorithm."; RL Bull. Math. Biol. 46:579-590(1984). RX Medline; 85073314. RX SeqAnalRef; DAVD8401. ADDRESS Dept. of Biochemical and Biophysical Sciences ADDRESS University of Houston, 4800 Calhoun ADDRESS Houston, Tx 77204-5934, USA CONTACT Dan Davison: dbd@theory.bchs.uh.edu SITE ftp anonymous ftp.bchs.uh.edu SITE Directory /gene-server/dos SITE-CONTACT dbd@theory.bchs.uh.edu SITE ftp anonymous ftp.bio.indiana.edu SITE Directory /molbio/ibmpc SITE-CONTACT gilbertd@cricket.bio.indiana.edu OS IBM PC or clone and PS/2, MS-DOS/PC-DOS, OS Vax/VMS, Sun-3 and Sun-4 Unix LANGUAGE C and FORTRAN VOLUME - AC BC00072 NAME TFASTA DOMAIN Alignment Search software DESCRIPTION Search DNA library for a protein sequence by DESCRIPTION translating the DNA sequence to protein DESCRIPTION in all six frames(three forward frames with DESCRIPTION the -3 command line option).TFASTA with ktup=2 DESCRIPTION is about as fast as a DNA FASTA with ktup=4, DESCRIPTION and is substantially more sensitive. AUTHOR William Pearson RT - ADDRESS U. of Virginia Dept. of Biochemistry CONTACT wrp@virginia.edu SITE ftp anonymous ftp.virginia.edu SITE Directory /pub/fasta = fasta(version number) SITE-CONTACT William Pearson wrp@virginia.edu OS all LANGUAGE - VOLUME - AC BC00073 NAME TNB DOMAIN Alignment Search software DESCRIPTION alignment tools.. DESCRIPTION lax - local alignment viewer for X11 DESCRIPTION lat - local alignment viewer for ASCII DESCRIPTION laps - local alignment viewer for PostScript DESCRIPTION align2dot - convert alignment to intermediate DESCRIPTION format DESCRIPTION dotplot - convert intermediate format to DESCRIPTION PostScript DESCRIPTION sim - pairwise local alignment program DESCRIPTION pab - convert pairwise alignments to multiple DESCRIPTION aligned blocks DESCRIPTION pblocks - construct aligned blocks for protein DESCRIPTION sequences DESCRIPTION dblocks - construct aligned blocks for DNA DESCRIPTION sequences AUTHOR Miller W, Schwartz Scott RA Boguski M.S., Hardison R.C., Schwartz S., Miller W.; RT "Analysis of conserved domains and sequence motifs in RT cellular regulatory proteins and locus control RT regions using new software tools for multiple RT alignment and visualization."; RL New Biol. 4:247-260(1992). RX Medline; 92256320. RX SeqAnalRef; BOGM9203. CONTACT webb@cse.psu.edu ADDRESS W. Miller ADDRESS Department of Computer Science and Engineering, ADDRESS The Pennsylvania State University, ADDRESS University Park, PA 16802, USA. SITE ftp anonymous groucho.cs.psu.edu SITE Directory /TNB SITE-CONTACT - OS - LANGUAGE - VOLUME - AC BC00074 NAME TREEALIGN DOMAIN Alignment Search software DOMAIN Phylogeny DESCRIPTION Multiple sequence alignment and phylogeny AUTHOR Hein J. RA Hein J.; RT "Unified approach to alignment and phylogenies."; RL Meth. Enzymol. 183:626-645(1990). RX Medline; 90190398. RX SeqAnalRef; HEIJ9001. ADDRESS - CONTACT - SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/unix UNIX software are stored SITE as archive (tar) files compressed (.Z). SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/vax VAX software are stored as SITE uuencoded (.UUE) files. SITE-CONTACT nethelp@ebi.ac.uk SITE ftp anonymous ftp.bchs.uh.edu (129.7.2.43)/ SITE Directory /pub/gene-server/unix SITE ftp anonymous ftp.bchs.uh.edu (129.7.2.43)/ SITE Directory /pub/gene-server/vms SITE-CONTACT Dan Davison: dbd@theory.bchs.uh.edu OS Unix, Vax/VMS LANGUAGE C VOLUME - AC BC00076 NAME XALIGN DOMAIN Alignment Search software DESCRIPTION xalign performs multiple sequence alignment based on DESCRIPTION homology and secondary structure. AUTHOR David Wishart, Robert Boyko RA Wishart D.S., Boyko R.F., Sykes B.D.; RT "Constrained multiple sequences alignment using XALIGN."; RT Comput. Appl. Biosci. 10(6):687-688(1994). RX SeqAnalRef; WISD9402. ADDRESS 7-13 HMRC ADDRESS University of Alberta, Edmonton, AB T6G 2S2, Canada CONTACT dsw@procyon.biochem.ualberta.ca, rbo@procyon.biochem.ualberta.ca CONTACT seqsee@procyon.biochem.ualberta.ca SITE ftp anonymous canopus.biochem.ualberta.ca SITE Directory /pub/ SITE-CONTACT - OS Unix (SUN and SGI) LANGUAGE Ansi C VOLUME - REQUIRES - AC BC00077 NAME XBLAST DOMAIN Alignment Search software DESCRIPTION module to read a BLAST output and to generate DESCRIPTION a filtered query AUTHOR Jean Michel Claverie RA Claverie J.-M., States D.J.; RT "Information enhancement methods for large scale sequence analysis."; RT Comput. Chem. 17:191-201(1993). RX SeqAnalRef; CLAJ9302. ADDRESS National Center for Biotechnology Information ADDRESS National Library of Medicine, Bldg. 38A, Room 8N-811 ADDRESS Bethesda, MD 20894, USA. CONTACT jmc@ncbi.nlm.nih.gov SITE ftp anonymous ncbi.nlm.nih.gov SITE Directory /pub/jmc SITE-CONTACT federhen@ncbi.nlm.nih.gov OS Unix LANGUAGE C VOLUME - AC BC00078 NAME XNU DOMAIN Alignment Search software DESCRIPTION program to read in sequences in Fasta format, DESCRIPTION test them for internal repeats and print them DESCRIPTION out with the internal repeats flagged AUTHOR Jean Michel Claverie RA Claverie J.-M., States D.J.; RT "Information enhancement methods for large scale sequence analysis."; RT Comput. Chem. 17:191-201(1993). RX SeqAnalRef; CLAJ9302. ADDRESS National Center for Biotechnology Information ADDRESS National Library of Medicine, Bldg. 38A, Room 8N-811 ADDRESS Bethesda, MD 20894, USA. CONTACT jmc@ncbi.nlm.nih.gov SITE ftp anonymous ncbi.nlm.nih.gov SITE Directory /pub/jmc SITE-CONTACT federhen@ncbi.nlm.nih.gov OS Unix LANGUAGE C VOLUME - AC BC00172 NAME STATALIGN DOMAIN Phylogeny DOMAIN Alignment Search software DESCRIPTION All widely-used methods of alignment and phylogeny inference DESCRIPTION make certain assumptions about sequence evolution. These DESCRIPTION assumptions may be implicit (e.g. the parsimony method for DESCRIPTION phylogeny reconstruction, the conventional dynamic programming DESCRIPTION algorithm for alignment inference) or they may be explicit. The DESCRIPTION methods implemented here are derived from evolutionary models DESCRIPTION with explicit assumptions. DESCRIPTION This set of programs estimates (via an expectation-maximization DESCRIPTION algorithm) parameters relevant to the evolutionary relationship DESCRIPTION between a pair of DNA or protein sequences. It performs DESCRIPTION pairwise alignment and allows reliability of alignment positions DESCRIPTION to be examined visually. Also, the phylogeny reconstruction DESCRIPTION method described in Thorne and Kishino (1992, MBE 9:1148-1162) DESCRIPTION is implemented. DESCRIPTION To understand these programs a bit better and find a list of DESCRIPTION relevant references, read the file ``statprogs.doc''. It may DESCRIPTION also be worthwhile to read the files ``arcs2ps.doc'' and DESCRIPTION ``trees.doc''. The latter two files respectively explain the DESCRIPTION alignment visualization and phylogeny reconstruction software. DESCRIPTION Use these programs at your own risk !! They can require massive DESCRIPTION amounts of computer time (don't attempt to use them if you don't DESCRIPTION have a workstation or better) and they are user-rude. A little DESCRIPTION familiarity with Unix, a computer that can compile C code, and DESCRIPTION ability to edit files are essential. Despite these drawbacks, DESCRIPTION the methods implemented here can yield comparatively accurate DESCRIPTION estimates of evolutionary parameters and relatively high quality DESCRIPTION alignments. DESCRIPTION For the most part, these programs were written by Jeff Thorne DESCRIPTION with intellectual help from Hirohisa Kishino, Gary Churchill, DESCRIPTION and Joseph Felsenstein. Sean Lamont and Kerry Neef supplied DESCRIPTION helpful programming tips. Leigh Thorne provided constructive DESCRIPTION comments. Programs not written by Jeff Thorne are part of the DESCRIPTION phylogeny inference package (PHYLIP) distributed by Joseph DESCRIPTION Felsenstein. Those programs from PHYLIP are noted in the DESCRIPTION following section. AUTHOR Jeff Thorne (see description for full list) RA Thorne J.L, Kishino H.; RL MBE 9:1148-1162(1992). ADDRESS Jeffrey Thorne ADDRESS Program in Statistical Genetics, Statistics Department ADDRESS North Carolina State University ADDRESS Raleigh NC 27695-8203, USA ADDRESS Tel: 1-(919) 515-1946 ADDRESS FAX: 1-(919) 515-7591 CONTACT thorne@stat.ncsu.edu SITE ftp anonymous ftp.bio.indiana.edu SITE Directory /molbio/evolve SITE-CONTACT D Gilbert: gilbertd@cricket.bio.indiana.edu OS Unix LANGUAGE C VOLUME - REQUIRES - 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 BC00381 NAME PairWise and SearchWise DOMAIN Sequence analysis DOMAIN Protein sequence analysis DOMAIN Alignment Search software DOMAIN Searching databases DESCRIPTION PairWise and SearchWise allow the comparison of a protein DESCRIPTION sequence or protein profile to a DNA sequence, allowing DESCRIPTION for frame shifts and introns within the DNA sequence. DESCRIPTION This allows for confident use of corrupted and genomic DESCRIPTION DNA data in bioinformatics projects. DESCRIPTION PairWise is the one-on-one alignment program DESCRIPTION SearchWise is the database searching program DESCRIPTION Opensearch is a mneu driven program to submit searchwise DESCRIPTION jobs AUTHOR Ewan Birney RT - ADDRESS Sanger Centre, Wellcome Trust Genome Campus ADDRESS Hinxton, Cambridge CB10 1RQ, UK CONTACT birney@sanger.ac.uk SITE ftp anonymous ftp.sanger.ac.uk SITE Directory /pub/birney/wise SITE-CONTACT root@sanger.ac.uk SITE WWW Server at URL http://www.sanger.ac.uk/~birney/wise/topwise.html OS VMS, IRIX, solaris, OSF/1 LANGUAGE C VOLUME - REQUIRES - COMMENTS SearchWise is CPU intensive AC BC00391 NAME BCM Search Launcher DOMAIN WWW server DOMAIN Sequence format conversion tools DOMAIN Sequence analysis DOMAIN Protein sequence analysis DOMAIN Protein structure analysis DOMAIN Structure prediction DOMAIN Pattern Identification DOMAIN Alignment Search software DOMAIN Alignment editing and display DOMAIN Alignment browser DOMAIN Restriction maps DOMAIN Database and analysis DOMAIN Searching databases DOMAIN Statistical significance DOMAIN Comparative analysis SERVER http://www.hgsc.bcm.tmc.edu/SearchLauncher/ DESCRIPTION The BCM Search Launcher is an integrated set of World- DESCRIPTION Wide Web (WWW) pages that organize molecular biology- DESCRIPTION related search and analysis services available on the DESCRIPTION WWW by function, and provide a single point-of-entry for DESCRIPTION related searches. The Protein Sequence Search Page, for DESCRIPTION example, provides a single sequence entry form for DESCRIPTION submitting sequences to WWW servers that provide remote DESCRIPTION access to a variety of different protein sequence search DESCRIPTION tools, including BLAST, FASTA, Smith-Waterman, BEAUTY, DESCRIPTION PROSITE, and BLOCKS searches. Other Launch pages provide DESCRIPTION access to 1) nucleic acid sequence searches, 2) multiple DESCRIPTION and pairwise sequence alignments, 3) gene feature searches, DESCRIPTION 4) protein secondary structure prediction, and 5) DESCRIPTION miscellaneous sequence utilities (e.g., 6-frame DESCRIPTION translation). The BCM Search Launcher also provides a DESCRIPTION mechanism to extend the utility of other WWW services by DESCRIPTION adding supplementary hypertext links to results returned DESCRIPTION by remote servers. For example, links to the NCBI's DESCRIPTION Entrez database and to the Sequence Retrieval System DESCRIPTION (SRS) are added to search results returned by the NCBI's DESCRIPTION WWW BLAST server. These links provide easy access to DESCRIPTION auxiliary information, such as Medline abstracts, that DESCRIPTION can be extremely helpful when analyzing BLAST database DESCRIPTION hits. For new or infrequent users of sequence database DESCRIPTION search tools, we have pre-set the default search parameters DESCRIPTION to provide the most informative first-pass sequence DESCRIPTION analysis possible. We have also developed a batch client DESCRIPTION interface for Unix and Macintosh computers that allows DESCRIPTION multiple input sequences to be automatically searched as DESCRIPTION a background task, with the results returned as individual DESCRIPTION HTML documents directly to the user's system. AUTHOR Randall F. Smith, Brent A. Wiese, Mary K. Wojzynski, AUTHOR Daniel B. Davison , and Kim C. Worley RA Smith R.F., Wiese B.A., Wojzynski M.K., Davison D.B., Worley K.C.; RT "BCM Search Launcher--An integrated interface to molecular RT biology database search and analysis services available on RT the World-Wide Web."; RL Submitted. ADDRESS Randall F. Smith, Ph.D. ADDRESS Department of Molecular and Human Genetics, T-921, ADDRESS Baylor College of Medicine ADDRESS One Baylor Plaza, Houston, TX 77030, USA ADDRESS Tel: +1 (713) 798-4735 Fax: +1 (713) 798-5386 CONTACT rsmith@bcm.tmc.edu CONTACT kworley@bcm.tmc.edu SITE WWW Server at URL http://www.hgsc.bcm.tmc.edu/SearchLauncher/ SITE-CONTACT rsmith@bcm.tmc.edu SITE WWW Server at URL http://dot.imgen.bcm.tmc.edu:9331/downloads/software/batch_client.html SITE give information about the downloads SITE ftp anonymous dot.imgen.bcm.tmc.edu for a batch client SITE Directory /pub/software/search-launcher OS Unix and Macintosh for the batch client LANGUAGE Perl (on Unix), AppleScript (on Macintosh) VOLUME - REQUIRES MacTCP on Macintosh and AppleScript, Perl on Unix AC 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 BC00395 NAME HMMER DOMAIN Alignment Search software DESCRIPTION Hidden Markov models (HMMs) of protein, DNA, or RNA primary DESCRIPTION structure consensus. Includes software for using HMMs DESCRIPTION to produce multiple sequence alignments, or for using DESCRIPTION HMMs for sensitive database searching for homologues DESCRIPTION of a sequence family. AUTHOR Sean R. Eddy RT - ADDRESS Dept. of Genetics ADDRESS Washington Univ. School of Medicine ADDRESS 660 S. Euclid Box 8232 ADDRESS St. Louis, MO 63110 CONTACT eddy@genetics.wustl.edu SITE ftp anonymous genome.wustl.edu SITE Directory /pub/eddy SITE-CONTACT eddy@genetics.wustl.edu SITE WWW Server at URL http://genome.wustl.edu/eddy/hmmer.html OS UNIX (SGI IRIX, SunOS, Solaris, DEC OSF/1, others) LANGUAGE ANSI C VOLUME - REQUIRES - AC BC00398 NAME SAM DOMAIN Alignment Search software DESCRIPTION A linear hidden Markov model is a sequence of nodes, each DESCRIPTION corresponding to a column in a multiple alignment. In our DESCRIPTION HMMs, each node has a match state (square), insert state DESCRIPTION (diamond) and delete state (circle). Each sequence uses a DESCRIPTION series of these states to traverse the model from start to DESCRIPTION end. Using a match state indicates that the sequence has a DESCRIPTION character in that column, while using a delete state DESCRIPTION indicates that the sequence does not. Insert states allow DESCRIPTION sequences to have additional characters between columns. In DESCRIPTION many ways, these models correspond to profiles. The DESCRIPTION primary advantage of these models over standard methods of DESCRIPTION sequence search is their ability to characterize an entire DESCRIPTION family of sequences. Thus, each position has a distribution DESCRIPTION of bases, as do transitions between states. That is, these DESCRIPTION linear HMMs have position-dependent character distributions DESCRIPTION and position-dependent insertion and deletion gap DESCRIPTION penalties. The alignment of each of a family to a trained DESCRIPTION model automatically yields a multiple alignment among those DESCRIPTION sequences. The SAM software system is a collection of DESCRIPTION tools for creating and using these models. AUTHOR David Haussler's group at UC Santa Cruz RA Haussler D., Krogh A., Mian S., Sjolander K.; RT "Protein Modeling Using Hidden Markov Models."; RL (In) C.I.S. Technical Report UCSC-CRL-92-23, RL University of California at Santa Cruz, 1992. RX SeqAnalRef; HAUD9201. RA Krogh A., Brown M., Mian I.S., Sjolander K., Haussler D.; RT "Hidden Markov Models in Computational Biology: RT Applications to Protein Modeling."; RL J. Mol. Biol. 235:1501-1531(1994). RX Medline; 94149699. RX SeqAnalRef; KROA9401. RA Baldi P., Chauvin Y., Hunkapiller T.; RT "Hidden Markov Models of Biological Primary Sequence Information."; RL Proc. Natl. Acad. Sci. U.S.A. 91:1059-1063(1994). RX Medline; 94134697. RX SeqAnalRef; BALP9401. RA Rabiner R.L.; RT "A Tutorial on Hidden Markov Models and Selected RT Applications in Speech Recognition."; RL Proc. IEEE 77:257-286(1989). RA Eddy S.R., Mitchison G., Durbin R.; RT "Maximum Discrimination Hidden Markov Models of Sequence RT Consensus."; RL J. Computational Biology, in press. RA Eddy S.R.; RT "Multiple Alignment Using Hidden Markov Models."; RL to be presented at ISMB '95, Cambridge, UK. ADDRESS Computer Engineering Board ADDRESS University of California ADDRESS Santa Cruz, CA 95064, USA. ADDRESS tel: +1 (408) 459-2939 - fax: +1 (408) 459-4829 CONTACT sam-info@cse.ucsc.edu SITE ftp anonymous ftp.cse.ucsc.edu SITE Directory /pub/protein/sam1.01.tar.Z.crypt SITE-CONTACT - OS Unix, MasPar LANGUAGE - VOLUME - REQUIRES - COMMENTS The source code is freely available in encrypted form COMMENTS send an email request to sam-info@cse.ucsc.edu to receive COMMENTS the Unix crypt key, or to make other arrangements if you COMMENTS do not have the Unix crypt program. AC BC00408 NAME SIM2 DOMAIN Alignment Search software DESCRIPTION This program build local alignments of two sequences, each DESCRIPTION of which may be hundreds of kilobases long. DESCRIPTION SIM2 first constructs n best non-intersecting chains of DESCRIPTION 'fragments', such as all occurrences of identical 5-tuples DESCRIPTION in each of two DNA sequences, for any specified n>= 1. DESCRIPTION Each chain is then refined by delivering an optimal DESCRIPTION alignment in a region delimited by the chain. AUTHOR Chao K-M, Zhang J., Ostell J. and Miller W. RA Chao K-M, Zhang J., Ostell J., Miller W.; RT "A local alignment tool for very long DNA sequences."; RL Comput. Appl. Bios. 11(2):147-153(1995). RX Medline; 95346409. RX SeqAnalRef; CHAK9501. ADDRESS (K-M Chao and W. Miller) ADDRESS Department of Computer Science and Engineering, ADDRESS The Pennsylvania State University, ADDRESS University Park, PA 16802, USA. ADDRESS (J. Zhang and J. Ostell) ADDRESS NCBI, NLM, NIH, Bethesda, MD 20894, USA. CONTACT zjing@sunset.nlm.nih.gov SITE ftp anonymous ncbi.nlm.nih.gov SITE Directory /pub/sim2 SITE-CONTACT zjing@sunset.nlm.nih.gov OS Unix, MacOS, Ms-Windows, Windows NT LANGUAGE C, NCBI software toolkit 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 BC00422 NAME DOTPLOT DOMAIN Alignment Search software DESCRIPTION We present an approach to the study of the relationships DESCRIPTION between biological sequences and structures applying imgae DESCRIPTION analysis methods to dotplots. We introduce a set of DESCRIPTION analytic tools based on different types of digital image DESCRIPTION processing filters that are new within the context of DESCRIPTION dotplots. We have reformulated some of the usual approaches DESCRIPTION in dotplot analysis as mathematical operations on images DESCRIPTION within the framework of mathematical morphology. An DESCRIPTION X-window based implementation of this new approach has been DESCRIPTION developed, and here is the source code. AUTHOR Oswaldo Trelles-Salazar(1), Emilio L. Zapata(1), AUTHOR Joaquin Dopazo(2), Andrew F.W. Coulson(3), AUTHOR and Jose Maria Carazo(1,2) RA Trelles-Salazar O., Zapata E.L., Dopazo J., RA Coulson A.F.W., Carazo J-M.; RT "An image-processing approach to dotplots: an RT X-Window-based program for interactive analysis RT of dotplots derived from sequence and structural data."; RL Comp. Appl. Biosci. 11(3):301-308(1995). ADDRESS (1) Computer Architecture Dept/University of Malaga,Spain ADDRESS (2) Biocomputing unit / Centro Nacional de Biotecnologia,Madrid,Spain ADDRESS (3) Biocomputing Research Unit, ICMB, University of Edinburgh,UK CONTACT carazo@samba.cnb.uam.es Jose Maria Carazo CONTACT ots@atc.ctima.uma.es Oswaldo Trelles-Salazar SITE ftp anonymous ftp.cnb.uam.es SITE Directory /software/molbio/dotplot SITE-CONTACT - OS Unix LANGUAGE C, X11 (Xview) VOLUME - REQUIRES the Xview library AC BC00480 NAME ProMSED (Protein Multiple Sequence Editor) DOMAIN Protein sequence analysis DOMAIN Alignment Search software DOMAIN Alignment editing and display DESCRIPTION ProMSED, Windows 3.x/95 application for multiple protein DESCRIPTION sequences alignment, alignment analysis and editing. DESCRIPTION Reads several sequence formats, has main functions similar DESCRIPTION to MS Word text editor. Automatic alignment is based on DESCRIPTION ClustulV algorithm; manual alignment and visual analysis DESCRIPTION are facilitated by group and block operations and amino DESCRIPTION acid color coding reflecting their similarity in physico- DESCRIPTION chemical, mutational and other properties. AUTHOR Anatoly Frolov, Alexey Eroshkin RA Frolov A., Eroshkin A.; RT "ProMSED: Protein Multiple Sequence Editor for Windows 3.x/95."; RL In preparation ADDRESS A. Frolov, A. Eroshkin ADDRESS Mol. Biol. Res. Inst. ADDRESS SRC VB VECTOR ADDRESS Koltsovo, Novosibirsk region ADDRESS 633159 REussdia CONTACT eroshkin@vector.nsk.su SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/dos/promsed/ SITE-CONTACT nethelp@ebi.ac.uk SITE ftp anonymous ftp.bionet.nsc.ru SITE Directory /pub/biology/vector/promsed.dem/ OS Windows 3.x/95 LANGUAGE C++ VOLUME 600 Kb REQUIRES - COMMENTS ProMSED is distributed as self-extracted archiuve. Demo COMMENTS version has limits on length and number of sequences. AC BC00483 NAME DBWATCHER DOMAIN Searching databases DOMAIN Alignment Search software DESCRIPTION DBWatcher is a program handling periodic BLAST searches to DESCRIPTION find similarities to your own sequences. It keeps track DESCRIPTION of the previous searches and only performs new ones when DESCRIPTION necessary (i.e. when the database has been updated, the DESCRIPTION sequence has been modified, or when settings have been DESCRIPTION changed). Only novel similarities are reported, thus DESCRIPTION saving the time of browsing through bulky result files. DESCRIPTION When executed daily (as a cron job) it ensures that you are DESCRIPTION informed as soon as new sequences similar to yours are DESCRIPTION incorporated into a given database. This is most valuable DESCRIPTION in association with an automatic database update DESCRIPTION procedure. Results are sent by electronic mail to one or DESCRIPTION several addresses making DBWatcher particularly suitable DESCRIPTION for collaborative database survey as well as for users who DESCRIPTION do not have access to locally maintained databases. DESCRIPTION From version 2.00, DBWatcher is also able to run as a DESCRIPTION Client of the NCBI BLAST Server for remote searches. AUTHOR Frederic Plewniak RT - ADDRESS CNRS - LGME 6520 ADDRESS I.G.B.M.C. ADDRESS B.P. 163 ADDRESS 67404 Illkirch Cedex - FRANCE CONTACT plewniak@igbmc.u-strasbg.fr SITE ftp anonymous ftp-igbmc.u-strasbg.fr SITE Directory /pub/DBWatcher SITE WWW server at http://www-igbmc.u-strasbg.fr/BioInfo/LocalDoc/DBWatcher SITE-CONTACT plewniak@igbmc.u-strasbg.fr OS Solaris, Digital Unix, Irix LANGUAGE ANSI C VOLUME <3Mb + log files REQUIRES BLAST programs and databases for local searches. REQUIRES NCBI ToolKit for remote searches as a BLAST Client. REQUIRES X/Motif libraries and the NCBI Vibrant ToolKit. COMMENTS The X and Vibrant libraries are only necessary for the COMMENTS companion program, SetDBwatcher, which provides a GUI COMMENTS to create and manage DBWatcher jobs. COMMENTS GCG's versions of the BLAST programs and databases can COMMENTS be used as well. AC BC00501 NAME WU-BLASTN DOMAIN Alignment Search software DOMAIN Searching databases DESCRIPTION Nucleotide query versus nucleotide sequence database search DESCRIPTION program, performing a 2-dimensional BLAST search with gaps DESCRIPTION and using Karlin-Altschul "Sum" statistics to evaluate DESCRIPTION the significance of the results; rapid and moderately sensitive; DESCRIPTION Washington University BLASTN version 2.0. AUTHOR Warren Gish RA Altschul S.F. and Gish W.; RT "Local alignment statistics."; RL Methods in Enzymology 266:460-80(1996). ADDRESS Dept. of Genetics ADDRESS Campus Box 8501 ADDRESS Washington University School of Medicine ADDRESS St. Louis MO 63108, USA CONTACT gish@watson.wustl.edu SITE WWW Server at URL http://blast.wustl.edu OS UNIX LANGUAGE C VOLUME - REQUIRES - COMMENTS No search services are provided by the WU-BLAST server. COMMENTS Users must download the software to run on their own server. AC BC00502 NAME WU-BLASTP DOMAIN Alignment Search software DOMAIN Searching databases DESCRIPTION Protein query versus protein sequence database search DESCRIPTION program, performing a 2-dimensional BLAST search with gaps DESCRIPTION and using Karlin-Altschul "Sum" statistics to evaluate DESCRIPTION the significance of the results; rapid and very sensitive; DESCRIPTION Washington University BLASTP version 2.0. AUTHOR Warren Gish RA Altschul S.F. and Gish W.; RT "Local alignment statistics."; RL Methods in Enzymology 266:460-80(1996). ADDRESS Dept. of Genetics ADDRESS Campus Box 8501 ADDRESS Washington University School of Medicine ADDRESS St. Louis MO 63108, USA CONTACT gish@watson.wustl.edu SITE WWW Server at URL http://blast.wustl.edu OS UNIX LANGUAGE C VOLUME - REQUIRES - COMMENTS No search services are provided by the WU-BLAST server. COMMENTS Users must download the software to run on their own server. AC BC00503 NAME WU-BLASTX DOMAIN Alignment Search software DOMAIN Searching databases DESCRIPTION Translated nucleotide query versus protein sequence database DESCRIPTION search program, performing a 2-dimensional BLAST search with DESCRIPTION gaps and using Karlin-Altschul "Sum" statistics to evaluate DESCRIPTION the significance of the results; rapid and moderately sensitive; DESCRIPTION Washington University BLASTX version 2.0. AUTHOR Warren Gish RA Altschul S.F. and Gish W.; RT "Local alignment statistics."; RL Methods in Enzymology 266:460-80 (1996). ADDRESS Dept. of Genetics ADDRESS Campus Box 8501 ADDRESS Washington University School of Medicine ADDRESS St. Louis MO 63108, USA CONTACT gish@watson.wustl.edu SITE WWW Server at URL http://blast.wustl.edu OS UNIX LANGUAGE C VOLUME - REQUIRES - COMMENTS No search services are provided by the WU-BLAST server. COMMENTS Users must download the software to run on their own server. AC BC00504 NAME WU-TBLASTN DOMAIN Alignment Search software DOMAIN Searching databases DESCRIPTION Protein query versus translated nucleotide sequence database DESCRIPTION search program, performing a 2-dimensional BLAST search with DESCRIPTION gaps and using Karlin-Altschul "Sum" statistics to evaluate DESCRIPTION the significance of the results; rapid and moderately sensitive; DESCRIPTION Washington University TBLASTN version 2.0. AUTHOR Warren Gish RA Altschul S.F. and Gish W.; RT "Local alignment statistics."; RL Methods in Enzymology 266:460-80(1996). ADDRESS Dept. of Genetics ADDRESS Campus Box 8501 ADDRESS Washington University School of Medicine ADDRESS St. Louis MO 63108, USA CONTACT gish@watson.wustl.edu SITE WWW Server at URL http://blast.wustl.edu OS UNIX LANGUAGE C VOLUME - REQUIRES - COMMENTS No search services are provided by the WU-BLAST server. COMMENTS Users must download the software to run on their own server. AC BC00505 NAME WU-TBLASTX DOMAIN Alignment Search software DOMAIN Searching databases DESCRIPTION Translated nucleotide query versus translated nucleotide sequence DESCRIPTION database search program, performing a 2-dimensional BLAST search DESCRIPTION with gaps and using Karlin-Altschul "Sum" statistics to evaluate DESCRIPTION the significance of the results; rapid and moderately sensitive; DESCRIPTION Washington University TBLASTX version 2.0. AUTHOR Warren Gish RA Altschul S.F. and Gish W.; RT "Local alignment statistics."; RL Methods in Enzymology 266:460-80(1996). ADDRESS Dept. of Genetics ADDRESS Campus Box 8501 ADDRESS Washington University School of Medicine ADDRESS St. Louis MO 63108, USA CONTACT gish@watson.wustl.edu SITE WWW Server at URL http://blast.wustl.edu OS UNIX LANGUAGE C VOLUME - REQUIRES - COMMENTS No search services are provided by the WU-BLAST server. COMMENTS Users must download the software to run on their own server. AC BC00514 NAME HCDSearch DOMAIN Sequence tools DOMAIN Alignment Search software DOMAIN Searching databases DESCRIPTION The Human cDNA Database (HCD) at the Institute for Genomic DESCRIPTION Research (TIGR) is the most complete, non-redundant, and DESCRIPTION structured collection of human expressed DNA sequences DESCRIPTION available to date (1997). Sequences and other data can be DESCRIPTION retrieved by users having open an account at HCD/TIGR. DESCRIPTION A HCD search involves composing and sending queries one DESCRIPTION by one and this can become time consuming if many queries DESCRIPTION must be sent. Moreover, a large amount of time is required DESCRIPTION thereafter to process the results. The HCDSearch system DESCRIPTION automatically composes and sends the queries by electronic DESCRIPTION mail using information provided in a text file; it also DESCRIPTION greatly accelerates results processing, generating lists of DESCRIPTION HCD numbers and library identifiers in a format that renders DESCRIPTION them very easy to examine. The programs run on Unix platforms. AUTHOR Laurentiu COCEA RA Cocea L.; RL "Search the Human cDNA Database at TIGT."; RT Comput. Appl. Biosci. 13(2):201-204(1997). ADDRESS Institut National de la Sante et de la Recherche Medicale ADDRESS Unite 373 ADDRESS Faculte de Medecine Necker, 8e etage ADDRESS Universite Descartes ADDRESS 156 rue de Vaugirard ADDRESS 75730 Paris CEDEX 15 ADDRESS FRANCE CONTACT cocea@infobiogen.fr CONTACT cocea@necker.fr SITE ftp anonymous iubio.bio.indiana.edu SITE Directory molbio/search files: hcd-search* SITE files: hcd-search* SITE-CONTACT gilbertd@bio.indiana.edu OS UNIX LANGUAGE Pascal VOLUME archive approx. 300 Kbyte REQUIRES - COMMENTS Files: hcd-search.1.0.tar.Z and hcd-search.readme. COMMENTS Compiled for UNIX 5.4 on Sun SPARC 2000. AC 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 BC00520 NAME Miropeats DOMAIN Sequence format conversion tools DOMAIN Sequence analysis DOMAIN Sequence tools DOMAIN Alignment Search software DOMAIN Alignment editing and display DESCRIPTION Miropeats is a graphical DNA sequence comparison tool. DESCRIPTION It can be used in almost all situations where one would DESCRIPTION normally use sequence alignments or dot plots to compare DESCRIPTION DNA sequences. However, Miropeats improves on dotplots DESCRIPTION in two ways, firstly, by allowing multiple sequences to DESCRIPTION be compared simultaneously and, secondly, by usually DESCRIPTION presenting a realtively intuitive graphic. It improves DESCRIPTION on large alignments by summarising all the similarities DESCRIPTION on a single page of PostScript (TM) graphics. AUTHOR Jeremy Parsons RA Parsons J.D.; RT "Miropeats: graphical DNA sequence comparisons."; RL Comput. Appl. Biosci. 11(6):615-619(1995). RA Parsons J.D.; RT "Improved tools for DNA comparison and clustering."; RL Comput. Appl. Biosci. 11(6):603-613(1995). ADDRESS European Bioinformatics Institute, ADDRESS Wellcome Trust Genome Campus, ADDRESS Hinxton, ADDRESS Cambridge ADDRESS CB10 1SD ADDRESS England CONTACT Jeremy.Parsons@ebi.ac.uk SITE WWW Server at URL http://genome.wustl.edu/est/esthmpg.html OS Solaris, IRIX, OSF, UNIX LANGUAGE C-shell, ANSI-C VOLUME - REQUIRES PostScript printing or viewing 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 BC00547 NAME SAGA DOMAIN Protein sequence analysis DOMAIN Alignment Search software SERVER http://www.ebi.ac.uk/~cedric DESCRIPTION SAGA (Sequence Alignmnet by Genetic ALgorithm) DESCRIPTION is a genetic algorithm designed for aligning protein DESCRIPTION sequences using various objective functions AUTHOR Notredame and Higgins RA Notredame C., Higgins D.; RT "SAGA: Sequence Alignmnet by Genetic Algorithm."; RL Nucleic Acids Res. 24(8):1515-1524(1996). ADDRESS Cedric NOTREDAME ADDRESS EMBL Outstation - The EBI ADDRESS Wellcome Trust Genome Campus, ADDRESS Hinxton, Cambridge CB10 1SD U.K. CONTACT cedric.notredame@ebi.ac.uk SITE WWW Server at URL http://www.ebi.ac.uk/~cedric OS UNIX LANGUAGE C VOLUME - REQUIRES - AC 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