Catalogue of Molecular Biology Programs Release 6.1 23 Jul 1999 All thanks are in the file biocatal.thanks. ===================================================================== AC BC00082 NAME AE2 DOMAIN Alignment editing and display DESCRIPTION AE2 is an alignment editor originally DESCRIPTION developed by T. J. Macke. AE2 was designed DESCRIPTION primarily for RNA/DNA sequence alignments, DESCRIPTION although it can be used successfully with DESCRIPTION proteins. AUTHOR T. J. Macke RT - ADDRESS University of Illinois, USA CONTACT - SITE ftp anonymous ftp.bio.indiana.edu SITE Directory /molbio/unix SITE-CONTACT Don Gilbert : gilbertd@cricket.bio.indiana.edu OS Unix LANGUAGE C VOLUME - AC BC00083 NAME ALSCRIPT DOMAIN Alignment editing and display DESCRIPTION Program to take a multiple protein sequence alignment DESCRIPTION and "prettify" it. Boxing, shading, font changes etc. AUTHOR Barton, G. J. (1993) RA Barton G.J.; RT "ALSCRIPT a tool to format multiple sequence alignments."; RL Protein Eng. 6:37-40(1993). RX Medline; 93165648. RX SeqAnalRef; BARG9301. 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 Barton, G. J.: gjb@bioch.ox.ac.uk SITE WWW server at URL http://geoff.biop.ox.ac.uk/manuals/alscript/alscript.html OS most Unix computers + VMS + MS-DOS. LANGUAGE ANSI-C VOLUME - AC BC00084 NAME BOXSHADE DOMAIN Alignment editing and display DESCRIPTION Plots multiple alignments, marking identical or DESCRIPTION similar residues AUTHOR Hofmann K. RT - ADDRESS - CONTACT - SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/vax VAX software are stored as SITE uuencoded (.UUE) files. SITE-CONTACT nethelp@ebi.ac.uk SITE ftp anonymous ftp.bio.indiana.edu SITE Directory /molbio/align SITE-CONTACT D Gilbert : gilbertd@cricket.bio.indiana.edu 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 - LANGUAGE Pascal VOLUME - AC BC00085 NAME DCSE DOMAIN Alignment editing and display DESCRIPTION Dedicated Comparative Sequence Editor DESCRIPTION It can be used to edit protein, DNA or RNA alignments. DESCRIPTION The structure of the molecules can be incorporated in the DESCRIPTION alignment DESCRIPTION Some of its features: DESCRIPTION - colouring of bases, amino acids, and secondary structure DESCRIPTION - easy menu interface (also key short-cuts) DESCRIPTION - automatic alignment relative to sequences already aligned DESCRIPTION with others DESCRIPTION - sequence grouping DESCRIPTION - can search for sequence, complement, sequence pattern. DESCRIPTION - split screen DESCRIPTION - marker system DESCRIPTION - checking of primary structure DESCRIPTION - checking of incorporated RNA structure DESCRIPTION - several ways for moving bases (or AA) or blocks of bases around DESCRIPTION - info on base composition, variability, ... DESCRIPTION - working on a limited set of organisms and positions DESCRIPTION - making a printable file DESCRIPTION - ASCII data files DESCRIPTION - multiple operating systems DESCRIPTION Convers is a complementary program to DCSE. It supports: DESCRIPTION - conversion from IG Suite, Genbank, EMBL, and PIR format DESCRIPTION - addition of new sequences to an alignment file from several DESCRIPTION formats DESCRIPTION - scanning of info in reference format AUTHOR Peter De Rijk RA De Rijk P., De Wachter R.; RT "DCSE v2.54, an interactive tool for sequence alignment and RT secondary structure research."; RL Comput. Appl. Biosci. 9:735-740(1993). RX Medline; 94192011. RX SeqAnalRef; DERP9301. ADDRESS University of Antwerp (UIA),Department of Biochemistry ADDRESS Universiteitsplein 1,B-2610 Antwerp, Belgium ADDRESS tel.: 32-03-820.23.16 fax: 32-03-820.22.48 CONTACT derijkp@reks.uia.ac.be SITE ftp anonymous uiam3.uia.ac.be (143.169.8.1) SITE Directory /pub/dcse SITE-CONTACT Peter De Rijk [*]: derijkp@reks.uia.ac.be SITE WWW server at URL http://rrna.uia.ac.be/dcse OS SGI LANGUAGE C,Tcl/Tk VOLUME - AC BC00086 NAME HOMOCHART DOMAIN Alignment editing and display DESCRIPTION Plotting multiple sequence alignments with DESCRIPTION boxes around identical residues AUTHOR Smith R. 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 SITE ftp anonymous ftp.bio.indiana.edu SITE Directory /molbio/align SITE-CONTACT D 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 - AC BC00087 NAME MALIGNED DOMAIN Alignment editing and display DESCRIPTION Multiple Sequence editor AUTHOR Clark S. RT - ADDRESS - CONTACT - SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/vax VAX software are stored as SITE uuencoded (.UUE) files. SITE-CONTACT nethelp@ebi.ac.uk SITE ftp anonymous ftp.bio.indiana.edu SITE Directory /molbio/vax 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/vms SITE-CONTACT Dan Davison: dbd@theory.bchs.uh.edu OS - LANGUAGE - VOLUME - AC BC00088 NAME MASE DOMAIN Alignment editing and display DESCRIPTION Don Faulkner and Jerzy Jurka's Multiple DESCRIPTION Aligned Sequence Editor (MASE), a full- DESCRIPTION screen sequence editor for aligning and DESCRIPTION displaying multiple sequences AUTHOR Faulkner D. V. J Jurka, RA Faulkner D.V., Jurka J.; RT "Multiple aligned sequence editor (MASE)."; RL Trends Biochem. Sci. 13:321-322(1988). RX Medline; 91134835. RX SeqAnalRef; FAUD8801. 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 ftp.ebi.ac.uk SITE Directory /pub/software/unix UNIX software are stored SITE as archive (tar) files compressed (.Z). SITE-CONTACT nethelp@ebi.ac.uk SITE ftp anonymous ftp.bchs.uh.edu (129.7.2.43)/ SITE Directory /pub/gene-server/unix SITE-CONTACT Dan Davison: dbd@theory.bchs.uh.edu SITE ftp anonymous mbcrr.harvard.edu SITE Directory /MBCRR_Package SITE-CONTACT Temple Smith : tsmith@mbcrr.harvard.edu OS Unix LANGUAGE C VOLUME - AC BC00089 NAME MSE DOMAIN Alignment editing and display DESCRIPTION Multiple Sequence editor AUTHOR Gilbert W.A. RT - ADDRESS - CONTACT - SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/vax VAX software are stored as SITE uuencoded (.UUE) files. SITE-CONTACT nethelp@ebi.ac.uk 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 BC00090 NAME NSEQTOOL DOMAIN Alignment editing and display DESCRIPTION simultaneous display of multiple sequence DESCRIPTION alignments and protein backbone structure. AUTHOR Schnobel R. RA Schnobel R.; RT "Integrated displays of aligned amino acid sequences and RT protein structures."; RL Comput. Appl. Biosci. 7:341-346(1991). RX Medline; 92004833. RX SeqAnalRef; SCHR9101. ADDRESS European Molecular Biology Laboratory, Heidelberg, FRG 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 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 SUN 4 or SPARCstation, colour graphics display LANGUAGE C SunView VOLUME - AC BC00091 NAME Sequence Logos DOMAIN Alignment editing and display DESCRIPTION A New Way to Display Consensus Sequences DESCRIPTION A logo is ``a single piece of type bearing two or more usually DESCRIPTION separate elements'' This logos are used to display aligned sets DESCRIPTION of sequences. Sequence logos concentrate the following DESCRIPTION information into a single graphic : DESCRIPTION The general consensus of the sequences. DESCRIPTION The order of predominance of the residues at every position. DESCRIPTION The relative frequencies of every residue at every position. DESCRIPTION The amount of information present at every position in the DESCRIPTION sequence, measured in bits. DESCRIPTION An initiation point, cut point, or other significant location DESCRIPTION (if appropriate). DESCRIPTION Any aligned set of DNA, RNA or protein sequences can be DESCRIPTION represented using this technique. AUTHOR Thomas D. Schneider and R. Michael Stephens RA Schneider T.D., Stephens R.M.; RT "Sequence logos: a new way to display consensus sequences."; RL Nucleic Acids Res. 18:6097-6100(1990). RX Medline; 91045074. RX SeqAnalRef; SCHT9001. ADDRESS National Cancer Institute, Frederick Cancer Research ADDRESS and Development Center, MD 21701, USA. CONTACT National Cancer Institute, Frederick Cancer Research and CONTACT Development Center, Laboratory of Mathematical Biology, CONTACT P.O. Box B, Frederick, MD 21701, USA. CONTACT toms@ncifcrf.gov and stephens@ncifcrf.gov. SITE ftp anonymous ftp.ncifcrf.gov SITE Directory /pub/delila SITE-CONTACT toms@ncifcrf.gov OS - LANGUAGE - VOLUME - AC BC00237 NAME GDE DOMAIN Sequence analysis DOMAIN Alignment editing and display DESCRIPTION Genetic Data Environement DESCRIPTION Ensemble de programmes d' analyse de sequences DESCRIPTION assemblage de contigs,recherches de DESCRIPTION similarites , analyses phylogenetiques AUTHOR Steven Smith AUTHOR S.W. Smith, R. Overbeek,C.R. Woese, W. Gilbert and P.M. Gillevet RA Smith S.W., Overbeek R., Woese C.R., Gilbert W., Gillevet P.M.; RT "The Genetic data environment and expandable GUI for multiple RT sequence analysis."; RT Comput. Appl. Biosci. 10(6):671-675(1994). RX SeqAnalRef; SMIS9401. ADDRESS - CONTACT Tim Littlejohn tim@bch.umontreal.ca SITE ftp anonymous megasun.BCH.UMontreal.CA Official SITE SITE Directory /pub SITE-CONTACT Tim Littlejohn tim@bch.umontreal.ca SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/unix UNIX software are stored SITE as archive (tar) files compressed (.Z). SITE-CONTACT nethelp@ebi.ac.uk SITE ftp anonymous ftp.bchs.uh.edu (129.7.2.43) SITE Directory /pub/gene-server/unix SITE-CONTACT Dan Davison: dbd@theory.bchs.uh.edu OS SUN Sparc-station (portage sur SGI, OS DECStation, Cray)system Unix, SunOS 4.1, OS OpenWindows 2.0 or MIT X11R4 LANGUAGE C VOLUME - COMMENTS Menu items for GDE are now available for the following programs COMMENTS from the FSAP package: COMMENTS NUMSEQ - sequence numbering, formatting & translation COMMENTS BACHREST - batch restriction site search. Now uses REBASE. COMMENTS P1HOM, - dot-matrix similarity searches for DNA and protein COMMENTS P2HOM,D3HOM,D4HOM COMMENTS These files are included in the file fsap.tar.Z in the directory COMMENTS psgendb at ftp.cc.umanitoba.ca. AC BC00368 NAME PRO-EXPLORE DOMAIN Molecular modelling and graphics DOMAIN Alignment editing and display DOMAIN Pattern Identification DESCRIPTION PRO-EXPLORE is a graphical protein modelling package. It DESCRIPTION provides tools for multi-sequence editing and alignment, DESCRIPTION sequence analysis, database investigation, and 3D modelling. AUTHOR - RT - ADDRESS OXFORD MOLECULAR, THE OXFORD SCIENCE PARK, OXFORD, OX4 4GA UK CONTACT Paul DAVIE , tel: +44 1865 784600 SITE - SITE-CONTACT - OS All Silicon Graphics (IRIX 4.0) LANGUAGE - VOLUME - REQUIRES PRO-EXPLORE package COMMENTS Silicon Graphics : gl_s run time library COMMENTS 24 bit planes for colour or RGB dithering COMMENTS 24 bit planes for Z-buffering COMMENTS ESV Graphics : PEX 2.0 COMMENTS Commercial software 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 BC00399 NAME SeqVu DOMAIN Alignment editing and display DESCRIPTION SeqVu is an alignment editor with analysis options that DESCRIPTION allows you to work quickly and simply with multiple DESCRIPTION sequences. It is ideal for manually correcting alignments DESCRIPTION produced using alignment software such as ClustalV. SeqVu DESCRIPTION goes beyond simple editing and allows you to produces DESCRIPTION publication quality figures, complete with outlined DESCRIPTION identity or homology. You can also shade residues which are DESCRIPTION of certain types, that have identity at a position, or are DESCRIPTION homologous. You can display outlining and shading DESCRIPTION simultaneously, so that you can see, for example, identity DESCRIPTION and homology simultaneously. There is also a novel DESCRIPTION hydropathy display which shows hydrophobicity on multiple DESCRIPTION sequences using coloured shading. Documents may be exported DESCRIPTION to graphics programs for further editing. AUTHOR James Gardner RT - ADDRESS Garvan Institute of Medical Research, ADDRESS Sidney, Australia CONTACT j.gardner@garvan.unsw.edu.au SITE ftp anonymous gimr.garvan.unsw.edu.au SITE Directory /pub SITE-CONTACT - OS MacOS LANGUAGE - VOLUME - REQUIRES - COMMENTS Shareware $US10. AC BC00409 NAME ShadyBox DOMAIN Alignment editing and display DESCRIPTION ShadyBox is a drawing program which DESCRIPTION enables you to box and shade regular and irregular DESCRIPTION shaped segments of aligned multiple sequences. It was DESCRIPTION designed with the intention of producing PostScript DESCRIPTION output suitable for use in publications. Version DESCRIPTION 2.0.1 was implemented with colour features. It is now DESCRIPTION possible to colour regions of sequences, individual DESCRIPTION residues or residues of specified frequency. Regions DESCRIPTION may be shaded with colour or the residues themselves DESCRIPTION may be coloured. GreyScale is available for those DESCRIPTION wishing to use it. ShadyBox accepts either an MSF DESCRIPTION (Multiple Sequence File), a Pretty or a Macaw DESCRIPTION formats. MSF files are produced by the GCG program DESCRIPTION Pileup or by ClustalW. Pretty files are produced by DESCRIPTION the GCG program Pretty and may include a consensus DESCRIPTION sequence. Macaw files are produced by the Macintosh DESCRIPTION multiple sequence alignment program, Macaw. ShadyBox DESCRIPTION allows you to generate a PostScript file in which you DESCRIPTION can display and print the box and shade regions. AUTHOR Camson Huynh RT - ADDRESS ANGIS (The Australian National Genomic Information Service) ADDRESS University of Sydney, ADDRESS Australia. CONTACT help@angis.su.oz.au SITE ftp anonymous morgan.angis.su.oz.au SITE Directory /pub/unix SITE-CONTACT - SITE WWW Server at URL http://morgan.angis.su.oz.au OS Unix LANGUAGE - VOLUME - REQUIRES Motif 1.X, X11 R4 or later COMMENTS ShadyBox has been tested and run successfully on SunOS 4.1.3 COMMENTS and Sun Solaris 2.X. It may run on other platforms aswell. AC BC00461 NAME DNA Stacks DOMAIN Sequence format conversion tools DOMAIN Sequence display DOMAIN Sequence editor DOMAIN Sequence analysis DOMAIN Sequence tools DOMAIN Protein sequence analysis DOMAIN Pattern Identification DOMAIN Alignment editing and display DOMAIN Alignment browser DOMAIN Genome Mapping Databases DOMAIN Phylogeny DESCRIPTION DNA Stacks (v. 1.1) is a HyperCard 2.x stack package DESCRIPTION for Macintosh computers featuring utilities for editing or DESCRIPTION coloring multiple DNA or protein sequence alignments, DESCRIPTION performing numerous data conversions or analyses related to DESCRIPTION molecular systematics, displaying auto-rescalable gene maps DESCRIPTION of mitochondrial or chloroplast genomes, extracting DNA DESCRIPTION gene sequences or translated protein sequences from about DESCRIPTION 26 animal mitochondrial genomes, and graphically depicting DESCRIPTION codon usage patterns. AUTHOR Eernisse, Douglas J. RA Eernisse, D. J.; RT "DNA Translator and Aligner: HyperCard utilities to aid RT phylogenetic analysis of molecules."; RL Comput. Appl. Biosci. 8:177-184(1992). RX Medline; 92274217. RX SeqAnalRef; EERD9201. ADDRESS D. J. Eernisse ADDRESS Dept. Biol. Sci. MH282 ADDRESS California State University ADDRESS Fullerton, CA 92634, USA CONTACT deernisse@fullerton.edu SITE ftp anonymous ftp.bio.indiana.edu SITE Directory /molbio/mac/ SITE-CONTACT archive@bio.indiana.edu SITE gopher Host: gopher://ftp.bio.indiana.edu Port: 70 SITE URL gopher://gopher://ftp.bio.indiana.edu:/70/11/IUBio-Software+Data/molbio/mac SITE WWW Server at URL http://biology.fullerton.edu/people/faculty/doug-eernisse/ OS MacOS LANGUAGE HyperTalk, C VOLUME 2 MB REQUIRES HyperCard 2.0 or greater, Macintosh AC BC00474 NAME LALNVIEW DOMAIN Sequence analysis DOMAIN Protein sequence analysis DOMAIN Alignment editing and display DESCRIPTION LALNVIEW is a graphical program for visualizing local DESCRIPTION alignments between two sequences (protein or nucleic acids). DESCRIPTION Sequences are represented by coloured rectangles to give DESCRIPTION an overall picture of their similarities. LALNVIEW is also DESCRIPTION able to display sequence features (active site, domain, DESCRIPTION motif, propeptide, etc.) along with the alignment. When DESCRIPTION using LALNVIEW through our Web servers, sequence features DESCRIPTION are automatically extracted from database annotations DESCRIPTION (SWISS-PROT, GenBank, EMBL or HOVERGEN) and displayed with DESCRIPTION the alignment. LALNVIEW is a useful tool for analysing DESCRIPTION pairwise sequence alignments and for making the link DESCRIPTION between sequence homology and what is known about the DESCRIPTION structure or function of these sequences. AUTHOR Laurent Duret RT - ADDRESS Department of Medical Biochemistry, ADDRESS University of Geneva, ADDRESS 1 rue Michel Servet, ADDRESS CH-1211 Geneva 4, Switzerland CONTACT duret@dim.hcuge.ch SITE ftp anonymous expasy.hcuge.ch SITE Directory /pub/lalnview SITE-CONTACT duret@dim.hcuge.ch SITE WWW Server at URL http://expasy.hcuge.ch/sprot/lalnview.html OS UNIX, PC, Macintosh LANGUAGE ANSI C, SUIT VOLUME 1 Mb REQUIRES color screen 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 BC00488 NAME GeneDoc DOMAIN Alignment editing and display DOMAIN Protein sequence analysis DOMAIN Phylogeny DESCRIPTION GeneDoc is a full featured Multiple Sequence Alignment Editor DESCRIPTION and Shading Utility. GeneDoc is also intended to help you bring DESCRIPTION your genetics research work to publication with lots of shading, DESCRIPTION page and font layout features. This is a utility that reads either DESCRIPTION .MSF Multiple Sequence alignment files or can Import Fasta Format DESCRIPTION files to be saved as a .MSF file project. DESCRIPTION GeneDoc is an alignment editor, that is it allows you to Edit the DESCRIPTION Alignment so that different residues from each sequence are lined DESCRIPTION up with each other. This is accomplished by moving the residues in DESCRIPTION one (or all but one) sequence relative to the other sequences by DESCRIPTION inserting or deleting gaps. GeneDoc also features the exclusive DESCRIPTION Grab and Drag mode, arranging residues like beads on a string. A DESCRIPTION residue editing mode is available to allow you to change the DESCRIPTION residues values themselves. Built in DayHoff and BlockSum scoring DESCRIPTION functions allow you to be sure your alignment changes are DESCRIPTION improving the score. Scores can be determined either by a Sum of DESCRIPTION Pairs method or with the Phylogenetic tree support. GUI DESCRIPTION implimentation makes it all so easy to use! DESCRIPTION GeneDoc also provides a comprehensive range of Display Shading DESCRIPTION Modes, functions and capabilities. Outlined below, these functions DESCRIPTION give flexible ways to look at the data and to show important DESCRIPTION concepts. Shading can even be done manually! DESCRIPTION GeneDoc provides output many different ways. You can print DESCRIPTION directly to the printer, export BitMaps, Text or MAC style Pict DESCRIPTION files. AUTHOR Karl Nicholas, Hugh Nicholas, PhD. RT - ADDRESS Karl Nicholas ADDRESS 566 Vallejo St. #34 ADDRESS San Francisco, CA, 94133 CONTACT ketchup@cris.com SITE WWW Server at URL http://www.cris.com/~ketchup/genedoc.shtml OS Win/3.1,Win/95,Win/NT LANGUAGE - VOLUME - REQUIRES - AC BC00497 NAME Sequin DOMAIN Sequence format conversion tools DOMAIN Sequence display DOMAIN Sequence editor DOMAIN Sequence analysis DOMAIN Sequence tools DOMAIN Alignment editing and display DOMAIN Alignment browser DOMAIN Sequence data submissions DESCRIPTION Sequin is a stand-alone software tool developed by the NCBI DESCRIPTION for submitting entries to the GenBank, EMBL, or DDBJ DESCRIPTION sequence databases. It is capable of handling simple DESCRIPTION submissions which contain a single short mRNA sequence, and DESCRIPTION complex submissions containing long sequences, multiple DESCRIPTION annotations, segmented sets of DNA, or phylogenetic and DESCRIPTION population studies. AUTHOR Jonathan Kans, Colombe Chappey RT - ADDRESS NIH/NLM/NCBI ADDRESS Building 38A, Room 8N805 ADDRESS Bethesda, MD 20894 ADDRESS U.S.A. CONTACT info@ncbi.nlm.nih.gov SITE ftp anonymous ncbi.nlm.nih.gov SITE Directory /sequin SITE-CONTACT info@ncbi.nlm.nih.gov SITE WWW Server at URL http://www.ncbi.nlm.nih.gov/Sequin OS Mac (68K and PPC), Windows (16 and 32 bit), Unix (Sun, Solaris, SGI, Linux, DEC) LANGUAGE English VOLUME - REQUIRES - COMMENTS Information about this package is available from COMMENTS http://www.ncbi.nlm.nih.gov/Sequin AC BC00498 NAME Map123d SERVER http://www-bio.lirmm.fr:8090/map123d.html DOMAIN WWW server DOMAIN Protein sequence analysis DOMAIN Protein structure analysis DOMAIN Structure prediction DOMAIN Alignment editing and display DOMAIN Molecular modelling and graphics SERVER http://www-bio.lirmm.fr:8090/map123d.html DESCRIPTION This server offers a set of tools for protein homology modelling. DESCRIPTION The "introduction" page provides a short overview on the DESCRIPTION problem of homology modelling and presents the tools DESCRIPTION available in this server: DESCRIPTION - Global multiple Alignment DESCRIPTION - Secondary structure prediction DESCRIPTION - Evaluation of a structural model AUTHOR H. Ripoche, J. Gracy, L. Chiche RT - ADDRESS LIRMM ADDRESS 161, Rue Ada ADDRESS 34392 MONTPELLIER Cedex 5 - France CONTACT hr@lirmm.fr SITE WWW Server at URL http://www-bio.lirmm.fr:8090/map123d.html OS - LANGUAGE - VOLUME - REQUIRES Java compatible browser (e.g. Netscape 2.0 or above) REQUIRES for some of the tools AC BC00509 NAME SEAVIEW DOMAIN Alignment editing and display DOMAIN Phylogeny DESCRIPTION A multiple sequence alignment editor DESCRIPTION Features: DESCRIPTION A graphical interface allows to edit alignment gaps DESCRIPTION in one or several sequences simultaneously. DESCRIPTION Lists of sequences and of sites can be built. DESCRIPTION The dot-plot method can be applied and used as a guide for DESCRIPTION manual alignment. DESCRIPTION If the CLUSTALW program is installed, SEAVIEW can run it DESCRIPTION on selected sequences and sites to have them aligned. DESCRIPTION Reads and writes alignment files in formats: CLUSTAL, DESCRIPTION PHYLIP, GCG's MSF, FASTA and MASE. AUTHOR Manolo Gouy RT - ADDRESS Laboratoire de biometrie, genetique et biologie des populations ADDRESS UMR CNRS 5558 ADDRESS Universite C. Bernard - Lyon 1 ADDRESS 69622 Villeurbanne, France CONTACT mgouy@biomserv.univ-lyon1.fr SITE ftp anonymous biom3.univ-lyon1.fr SITE Directory /pub/mol_phylogeny/seaview SITE-CONTACT - OS Sun/Solaris, Sun/SunOs, DEC/Alpha, HP, OS SGIr5-IRIX, IBM-AIX, linux on 386/486/586 processors 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 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 BC00568 NAME JOY SERVER http://www-cryst.bioc.cam.ac.uk/cgi-bin/joy.cgi DOMAIN Protein sequence analysis DOMAIN Protein structure analysis DOMAIN Alignment editing and display DOMAIN WWW server DOMAIN Comparative analysis DESCRIPTION JOY is a program to annotate protein sequence alignments DESCRIPTION with three-dimensional (3D) structural features. It was DESCRIPTION developed to display 3D structural information in a sequence DESCRIPTION alignment and to help understand the conservation of amino DESCRIPTION acids in their specific local environments. The JOY DESCRIPTION representation now constitutes an essential part of the two DESCRIPTION databases of protein structure alignments: HOMSTRAD DESCRIPTION (http://www-cryst.bioc.cam.ac.uk/~homstrad) and CAMPASS DESCRIPTION (http://www-cryst.bioc.cam.ac.uk/~campass). It has also been DESCRIPTION successfully used for identifying distant evolutionary DESCRIPTION relationships. DESCRIPTION DESCRIPTION JOY takes an input alignment (or a single sequence) in a DESCRIPTION format similar to that of the NBRF/PIR format and produces a DESCRIPTION number of output files, including the annotated alignment in DESCRIPTION PostScript, LATEX and HTML. JOY requires a series of DESCRIPTION datafiles containing information about secondary structures, DESCRIPTION solvent accessibility and hydrogen bonding. These are DESCRIPTION produced automatically from a PDB file by supporting DESCRIPTION programs. AUTHOR Kenji Mizuguchi, Charlotte M. Deane, Tom L. Blundell, AUTHOR Mark S. Johnson, John P. Overington RA Mizuguchi K., Deane C.M., Johnson M.S., Blundell T.L., Overington J.P.; RT "JOY: protein sequence-structure representation and analysis."; RL Bioinformatics 14:617-623(1998). ADDRESS Department of Biochemistry ADDRESS University of Cambridge ADDRESS 80 Tennis Court Road ADDRESS Cambridge CB2 1GA ADDRESS UK CONTACT kenji@cryst.bioc.cam.ac.uk SITE WWW Server at URL http://www-cryst.bioc.cam.ac.uk/cgi-bin/joy.cgi OS UNIX LANGUAGE Fortran, C, Perl VOLUME - REQUIRES - COMMENTS Currently only executable files for IRIX5.3 or highter are COMMENTS available, but distribution of the source code to academic COMMENTS users will follow. AC BC00587 NAME BioEdit DOMAIN Sequence format conversion tools DOMAIN Sequence display DOMAIN Sequence editor DOMAIN Sequence analysis DOMAIN RNA analysis DOMAIN Alignment editing and display DOMAIN Alignment browser DOMAIN Searching databases DOMAIN General tools DESCRIPTION BioEdit is a user-friendly, graphically-oriented sequence DESCRIPTION alignment editor for Windows 95/98/NT. Features include DESCRIPTION several modes of hand alignment, auto-linking to ClustalW, DESCRIPTION user-defined color view (editable by mouse point- and DESCRIPTION click), separate amino acid and nucleotide color tables, DESCRIPTION Shaded views with many options, RNA comparative analysis DESCRIPTION tools (including mutual information with interactive 2-D DESCRIPTION matrix plots and area plots), restriction mapping, browsing DESCRIPTION restriction enzymes by company, easy plasmid drawing and DESCRIPTION annotation, protein hydropathy plots, can handle very large DESCRIPTION alignments (up to 20000 sequences of undefined length), DESCRIPTION several translation modes, nucleotide/translation toggling DESCRIPTION for alignment in both protein and DNA views, 6-frame DESCRIPTION translations, basic sequence manipulations (complement, DESCRIPTION reverse, uppercase, lowercase), internal web browser (HTML DESCRIPTION 2.0-compliant), auto-link to external browser with internet DESCRIPTION bookmarks, on-line help system, configure external apps via DESCRIPTION a graphical interface to automatically run through a DESCRIPTION BioEdit interface, split-window views for editing of two DESCRIPTION different places in an alignment at the same time, local DESCRIPTION NCBI BLAST accessories, single sequence editing and DESCRIPTION manipulation, retains GenBank data (eg, FEATURES, DESCRIPTION REFERENCE, SOURCE, PID or NID, etc), binary file format for DESCRIPTION fast save/open of very large files (alignments up to 100 Mb DESCRIPTION and more are no problem), correct spacing of all available DESCRIPTION fonts in edit window and in shaded view, creation of DESCRIPTION high-quality alignment figures via shading with many DESCRIPTION options (including full-color, id/sim shading, enhanced DESCRIPTION metafile copy and paste directly into graphics programs), DESCRIPTION easy formatted text print preview. AUTHOR Tom Hall RT - ADDRESS Department of Microbiology, ADDRESS North Carolina State University ADDRESS Raleigh, NC 27695 CONTACT tahall2@unity.ncsu.edu SITE WWW Server at URL http://www.mbio.ncsu.edu/RNaseP/info/programs/BIOEDIT/bioedit.html OS Windows LANGUAGE - VOLUME BioEdit.zip file = 7.6 Mb REQUIRES Windows 95, 98 or NT, Pentium 60+, 16 Mb RAM+, REQUIRES 20 Mb hard drive space AC BC00588 NAME DAMBE (Data analysis in molecular biology and evolution) DOMAIN Sequence format conversion tools DOMAIN Sequence display DOMAIN Sequence analysis DOMAIN Sequence tools DOMAIN Protein sequence analysis DOMAIN Protein structure analysis DOMAIN Alignment editing and display DOMAIN Alignment browser DOMAIN Genetic tools DOMAIN Molecular Evolution DOMAIN Phylogeny DOMAIN Database and analysis DOMAIN Searching databases DOMAIN General tools DOMAIN Statistical significance DOMAIN Comparative analysis DESCRIPTION DAMBE (Data Analysis in Molecular Biology DESCRIPTION and Evolution) is an integrated software package for DESCRIPTION converting, manipulating, statistically and graphically DESCRIPTION describing and analyzing molecular sequence data, with a DESCRIPTION user-friendly Windows 95 interface. AUTHOR Xuhua Xia RT - ADDRESS Department of Ecology & Biodiversity, ADDRESS University of Hong Kong, Hong Kong CONTACT xxia@hkusua.hku.hk SITE WWW Server at URL http://web.hku.hk/~xxia/software/software.htm OS Windows 95 LANGUAGE - VOLUME 10 MB REQUIRES Windows 95 AC BC00590 NAME FASTA SCAN DOMAIN Sequence format conversion tools DOMAIN Sequence tools DOMAIN GCG tools DOMAIN Alignment editing and display DOMAIN Alignment browser DESCRIPTION FASTA SCAN allow you to select and save sequences of real DESCRIPTION interest from a FASTA output. DESCRIPTION This version was successfully tested with: DESCRIPTION - FASTA of GCG package (v.8.1 and 10) DESCRIPTION - FASTA of "Pearson package" version 3.1t07 May, 1998 DESCRIPTION The maximum number of sequences is 1000. AUTHOR Olivier Friard RT - ADDRESS Dipartimento di Genetica, Biologia e Biochimica ADDRESS via Santena, 5bis ADDRESS I-10126 TURIN ITALY CONTACT friard@molinette.unito.it SITE WWW Server at URL http://pcgen018.molinette.unito.it/programs.html OS win95, win98, NT 4.0 LANGUAGE - VOLUME - REQUIRES - AC BC00601 NAME Jalview DOMAIN Sequence display DOMAIN Sequence analysis DOMAIN Protein sequence analysis DOMAIN Alignment editing and display DOMAIN Alignment browser DOMAIN JAVA DOMAIN Multivariate analysis DOMAIN WWW server SERVER http://circinus.ebi.ac.uk:6543/jalview DESCRIPTION A multiple sequence alignment viewer and editor. Alignments DESCRIPTION can be divided into subfamilies using a tree or by hand. DESCRIPTION Conservation can then be calculated using physico-chemical DESCRIPTION properties within subfamilies or across the whole alignment. DESCRIPTION Principal component analysis can also be used as an DESCRIPTION alternative way of clustering the sequences. An SRS server DESCRIPTION can be used to fetch and display the sequence features and DESCRIPTION any PDB structures listed. There is limited access to DESCRIPTION external programs including clustalw and jnet secondary DESCRIPTION structure prediction. AUTHOR Michele Clamp RT - ADDRESS The Sanger Centre ADDRESS Wellcome Trust Genome Campus ADDRESS Hinxton ADDRESS Cambs. ADDRESS CB10 1SA ADDRESS UK CONTACT michele@sanger.ac.uk SITE WWW Server at URL http://circinus.ebi.ac.uk:6543/jalview OS - LANGUAGE java1.1 VOLUME 300kb REQUIRES Java runtime environment