Catalogue of Molecular Biology Programs Release 6.1 23 Jul 1999 All thanks are in the file biocatal.thanks. ===================================================================== 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 BC00416 NAME CAIC DOMAIN Phylogeny DOMAIN Comparative analysis DESCRIPTION CAIC - a comparative analysis package for the Apple DESCRIPTION Macintosh. This application implements a suite of DESCRIPTION 'phylogenetically correct' comparative methods for DESCRIPTION data sets including continuous variables. AUTHOR Andy Purvis, Andrew Rambaut RA Purvis A., Rambaut A.; (1995) RT "Comparative analysis by independent contrasts (CAIC): RT an Apple Macintosh application for analysing comparative RT data."; RL Comp. Appl. in Biosci. 11(3):247-251(1995). ADDRESS Department of Zoology, University of Oxford ADDRESS South Parks Road, Oxford OX1 4JD, U.K. CONTACT andy.purvis@zoo.ox.ac.uk SITE ftp anonymous evolve.zps.ox.ac.uk SITE Directory /FTP/packages/CAIC SITE-CONTACT andrew.rambaut@zoo.ox.ac.uk SITE WWW Server at URL http://evolve.zps.ox.ac.uk/CAIC/CAIC.html OS MacOS LANGUAGE - VOLUME - REQUIRES System 6.0, 500Kb RAM AC BC00435 NAME BEAUTY DOMAIN Sequence analysis DOMAIN Sequence tools DOMAIN Protein sequence analysis DOMAIN Database and analysis DOMAIN Searching databases DOMAIN Statistical significance DOMAIN Comparative analysis DOMAIN WWW server DESCRIPTION BEAUTY (BLAST Enhanced Alignment Utility) is an enhanced DESCRIPTION version of the NCBI's BLAST database search tool that DESCRIPTION facilitates identification of the functions of matched DESCRIPTION sequences. We have created new databases of conserved DESCRIPTION regions and functional domains for protein sequences in DESCRIPTION the NCBI's Entrez database, and BEAUTY allows this DESCRIPTION information to be directly incorporated into BLAST search DESCRIPTION results. A Conserved Regions Database, containing the DESCRIPTION locations of conserved regions within Entrez protein DESCRIPTION sequences, was constructed by 1) clustering the entire DESCRIPTION database into families, 2) aligning each family using our DESCRIPTION PIMA multiple sequence alignment program, and then DESCRIPTION 3) scanning the multiple alignments to locate the DESCRIPTION conserved regions within each aligned sequence. A DESCRIPTION separate Annotated Domains Database was constructed by DESCRIPTION extracting the locations of all annotated domains and DESCRIPTION sites from sequences represented in the Entrez, PROSITE, DESCRIPTION BLOCKS, and PRINTS databases. BEAUTY performs a BLAST DESCRIPTION search of those Entrez sequences with conserved regions DESCRIPTION and/or annotated domains. BEAUTY then uses the DESCRIPTION information from the Conserved Regions and Annotated DESCRIPTION Domains databases to generate, for each matched sequence, DESCRIPTION a schematic display that allows one to directly compare DESCRIPTION the relative locations of 1) the conserved regions, DESCRIPTION 2) annotated domains and sites, and 3) the locally-aligned DESCRIPTION regions matched in the BLAST search. In addition, BEAUTY DESCRIPTION search results include World-Wide Web hypertext links to DESCRIPTION a number of external databases that provide a variety of DESCRIPTION additional types of information on the function of matched DESCRIPTION sequences. This convenient integration of protein DESCRIPTION families, conserved regions, annotated domains, alignment DESCRIPTION displays, and World-Wide Web resources greatly enhances DESCRIPTION the biological informativeness of sequence similarity DESCRIPTION searches. Beauty searches can be performed remotely on DESCRIPTION our system using the "BCM Search Launcher" World-Wide-Web pages AUTHOR Kim C. Worley, Brent A. Wiese, and Randall F. Smith RA Worley K.C., Wiese B.A., Smith R.F.; RT "BEAUTY: An enhanced BLAST-based search tool that RT integrates multiple biological information resources RT into sequence similarity search results."; RL Genome Research 5:173-184 (1995). ADDRESS Kim C. Worley, Ph.D. ADDRESS Department of Molecular and Human Genetics ADDRESS T-929, Baylor College of Medicine ADDRESS One Baylor Plaza, Houston, TX 77030, USA ADDRESS Phone: +1 (713) 798-8292 FAX: +1 (713) 798-5386 CONTACT kworley@bcm.tmc.edu CONTACT brent@bcm.tmc.edu CONTACT rsmith@bcm.tmc.edu SITE WWW server at URL http://gc.bcm.tmc.edu:8088/search-launcher/launcher.html SITE-CONTACT rsmith@bcm.tmc.edu SITE ftp anonymous gc.bcm.tmc.edu for a batch client SITE Directory /pub/software/search-launcher OS Unix and Macintosh for the batch client LANGUAGE Perl (on Unix), AppleScript (on Macintosh) VOLUME - REQUIRES MacTCP on Macintosh and AppleScript, Perl on Unix AC BC00469 NAME OSA DOMAIN Sequence analysis DOMAIN Protein sequence analysis DOMAIN Epidemiology DOMAIN Phylogeny DOMAIN Statistical significance DOMAIN Comparative analysis DESCRIPTION OSA is a program to find, within an alignment of DESCRIPTION large sequences, those regions with an informative content DESCRIPTION similar to the displayed by the whole alignment and select, DESCRIPTION among them, the shortest empiricaly significant ones. The use of DESCRIPTION these short regions, instead of the larger ones, can save a DESCRIPTION considerable amount of time and resources in molecular screening DESCRIPTION or molecular epidemiology studies. AUTHOR Maria Jesus Martin, Joaquin Dopazo RA Martin M.J., Gonzalez-Candelas F., Sobrino F., Dopazo J.; RT "A method for determining the position and size of optimal RT sequence regions for phylogenetic analysis."; RL J. Mol. Evol. 41:1128-1138(1995). ADDRESS R&D Department, TDI ADDRESS c/ Condes de Torreanaz, 5 ADDRESS 28028, Madrid ADDRESS SPAIN CONTACT martin@tdi.es CONTACT dopazo@tdi.es SITE ftp anonymous ftp.tdi.es SITE Directory /pub/programas/ SITE-CONTACT martin@tdi.es SITE WWW Server at URL http://www.tdi.es/programas/osa-i.htm OS UNIX (Solaris, Irix) LANGUAGE GPC Pascal VOLUME 300K REQUIRES GPC for compiling sources COMMENTS OSA is available as both : executable file for Solaris or COMMENTS Irix operating systems and sources files. GPC compiler is COMMENTS only necessary if you download the sources. AC BC00515 NAME DROSOPOSON DOMAIN Genetic tools DOMAIN Population Genetics DOMAIN Database and analysis DOMAIN Statistical significance DOMAIN Comparative analysis DESCRIPTION An object-oriented knowledge base dedicated DESCRIPTION on localisation data of transposable element insertions DESCRIPTION along the polytene chromosomes of Drosophila. The base DESCRIPTION brings together: DESCRIPTION 1) data available on chromosomal localisations of DESCRIPTION transposable element insertions and on features of the DESCRIPTION polytene chromosomes (DNA content, recombination rate, DESCRIPTION breakpoints...), 2) some statistical methods aimed at DESCRIPTION analysing the distribution of the transposable element DESCRIPTION insertions along the chromosomes, in relation with the DESCRIPTION chromosome features. DROSOPOSON can thus be used either as DESCRIPTION a consultation tool, as an instant look of the available DESCRIPTION knowledge, or to analyse user's data. AUTHOR Christine HOOGLAND RA Hoogland C., Biemont C.; RT "DROSOPOSON: a knowledge base on chromosomal localization of RT transposable element insertions in Drosophila."; RL Compu. Appl. Biosci. 13:61-68(1997). ADDRESS Laboratoire de Biometrie, Genetique et Biologie des populations ADDRESS UMR CNRS 5558 ADDRESS Universite C. Bernard - Lyon 1 ADDRESS 69622 Villeurbanne ADDRESS France CONTACT hoogland@biomserv.univ-lyon1.fr SITE ftp anonymous biom3.univ-lyon1.fr SITE Directory /pub/drosoposon SITE-CONTACT - OS Sun/Solaris LANGUAGE LE_LISP VOLUME - REQUIRES - COMMENTS Commercial softwares needed: Le_Lisp and Aida by ILOG (ILOG SA, Gentilly, France); COMMENTS Knowledge base manager: SHIRKA developed by INRIA and the ARTEMIS laboratory in Grenoble, COMMENTS France (Francois.Rechenmann@inria.fr). COMMENTS All the files (data, programs, schemes) are available independently, as plain text. AC 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 BC00570 NAME RASA 2.2 DOMAIN Sequence analysis DOMAIN Structure prediction DOMAIN Pattern Identification DOMAIN Phylogeny DOMAIN Statistical significance DOMAIN Comparative analysis DESCRIPTION RASA 2.2 provides a set of tools for measuring DESCRIPTION phylogenetic signal and for studying its distribution DESCRIPTION among taxa. DESCRIPTION DESCRIPTION This software is used for DESCRIPTION * measuring signal DESCRIPTION * testing the suitability of available outgroup taxa DESCRIPTION * detecting long branches in the taxon variance plot DESCRIPTION * performing the mixed-character taxon test for differential DESCRIPTION lineage sorting DESCRIPTION * performing bootstrap power and effect to examine the DESCRIPTION power curve for your data. DESCRIPTION DESCRIPTION Exploratory options include DESCRIPTION * determining the signal spectrum for a set of sequences DESCRIPTION * removing noisy sites DESCRIPTION DESCRIPTION Some researchers have used the software to examine DESCRIPTION hypotheses of alignment using phylogenetic signal as the DESCRIPTION criterion. DESCRIPTION DESCRIPTION This software can be used on discrete data (molecular, DESCRIPTION morphological, or mixed). AUTHOR James Lyons-Weiler, PhD RA Lyons-Weiler, J., Hoelzer, G.A. and Tausch R.J.; RT "Relative Apparent Synapomorphy Analysis (RASA) I: RT the statistical measurement of phylogenetic signal."; RL Molecular Biology and Evolution 13:749-757(1996). RA Lyons-Weiler, J. and Milinkovitch, M.C.; RT "A phylogenetic approach to the problem of differential RT lineage sorting."; RL Molecular Biology and Evolution 14:968-975(1997). RA Lyons-Weiler, J. and Hoelzer, G.A.; RT "Escaping from the Felsenstein Zone by detecting long RT branches in phylogenetic data."; RL Molecular Phylogenetics and Evolution 8:375-384(1997). RA Lyons-Weiler, J. and Hoelzer, G.A.; RL "Optimal outgroup analysis."; RL Biological Journal of the Linnean Society 64:493(1998). RA Milinkovitch, M.C. and Lyons-Weiler, J.; RT "Finding optimal outgroup topologies and convexities RT when the choice of outgroups is not obvious."; RL Molecular Phylogenetics and Evolution 9:348-357(1998). ADDRESS - CONTACT jfl8@psu.edu SITE WWW Server at URL http://test1.bio.psu.edu/LW/list.htm OS Mac/PowerPC REQUIRES All superfluous extensions off. COMMENTS The software will be updated and bugs fixed at COMMENTS irregular intervals. Watch for updates. 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 BC00594 NAME Protein Adviser for Windows DOMAIN Sequence format conversion tools DOMAIN Sequence display DOMAIN Protein sequence analysis DOMAIN Protein structure analysis DOMAIN Molecular modelling and graphics DOMAIN General tools DOMAIN Chemistry DOMAIN Image analysis DOMAIN Comparative analysis DOMAIN Protein 3D visualisation, editing and analysis (QSAR) DESCRIPTION FQS Protein Adviser displays and analyses 3D structures of DESCRIPTION biological molecules such as proteins or nucleic acids. DESCRIPTION Protein Adviser is a powerful tool for visual and numerical DESCRIPTION investigation of protein molecules and their 3D structures. DESCRIPTION The new implementation for Windows 95/98 and NT uses the DESCRIPTION innovative Microsoft technology for rendering molecular DESCRIPTION graphics known as Direct3D. Using Direct 3D technology FQS DESCRIPTION created the fastest biomolecular viewer available on PC DESCRIPTION platform. DESCRIPTION Versatile features to support protein analysis: DESCRIPTION - sequence based 3D analysis DESCRIPTION - Three level selections: atoms, residues, molecules DESCRIPTION - Display/Hide hydrogen's DESCRIPTION - Display/Hide side chain DESCRIPTION - Hydrogen generation DESCRIPTION - Measure atom-atom distances DESCRIPTION - Compare 3D structures DESCRIPTION - Compare aminoacid sequences DESCRIPTION - Analyze Ramachandran plots DESCRIPTION - Mutate and change side chain conformations DESCRIPTION - Build proteins, change torsional angles DESCRIPTION - Copy and paste molecules between the windows DESCRIPTION - Rotate and move selected molecules DESCRIPTION Windows specific features DESCRIPTION Protein Adviser can open as many documents DESCRIPTION as you wish and analyse them within one program session, DESCRIPTION Protein Adviser implements full ActiveX/OLE2 functionality. DESCRIPTION Its objects (molecules) may be placed on your WEB page and DESCRIPTION visualized by your colleagues everywhere through the DESCRIPTION internet. DESCRIPTION Plotting hydrophobicity and other properties DESCRIPTION Protein Adviser for Windows can plot DESCRIPTION different named properties. The program comes with 3 DESCRIPTION different scales of hydrophobicty, including Kyte&Doolittle DESCRIPTION scale. The program includes also 6 other predefined QSAR DESCRIPTION methods. DESCRIPTION Plotting Ramachandran diagrams DESCRIPTION Ramachandran plots show two-dimensional DESCRIPTION histograms of the values of conformational angles phi and DESCRIPTION psi. These histograms are superimposed on the areas of DESCRIPTION allowed and forbidden conformational angles pair values. DESCRIPTION Aminoacids DESCRIPTION Protein Adviser displays sequences of DESCRIPTION aminoacids as 3-letter codes, 1-letter codes or secondary DESCRIPTION structure symbols DESCRIPTION Protein's 3D structure comparison DESCRIPTION Protein Adviser for Windows allows for DESCRIPTION protein structure comparison command. The program DESCRIPTION superimposes the protein's 3D structures based on C(alpha) DESCRIPTION atoms coordinates and RMSD analysis. AUTHOR FQS Ltd. (Fujitsu Kyushu System Engineering Ltd.) RT - ADDRESS FQS Poland Sp. z o.o. ADDRESS Palac Pugetow ADDRESS ul. Starowislna 13-15 ADDRESS 31-038 Krakow ADDRESS Poland ADDRESS Tel. (+48 12) 4294345 ADDRESS Fax. (+48 12) 4296124 CONTACT info@fqspl.com.pl SITE WWW Server at URL http://www.fqspl.com.pl/protein OS Windows 95/98/NT, Macintosh LANGUAGE English, Japanese VOLUME 10 MB REQUIRES PC Pentium 166, 16MB RAM, Microsoft DirectX COMMENTS Commercial software. COMMENTS Price: COMMENTS 800 USD - commercial license & COMMENTS 400 USD - academic licence .