Catalogue of Molecular Biology Programs Release 6.1 23 Jul 1999 All thanks are in the file biocatal.thanks. ===================================================================== AC BC00545 NAME GRS DOMAIN Genome Analysis DESCRIPTION GRS is a graphic tool for retrieval and visualization DESCRIPTION of genome segments from partially or completely sequenced genomes. AUTHOR Thomas Sicheritz-Pontn, Siv G.E. Andersson RA Sicheritz-Pontn T., S.G.E. Andersson RT "GRS: A Graphic Tool for Genome Retrieval and Segment Analysis."; RL MICROBIAL & COMPARITIVE GENOMICS 2:123-139(1997). ADDRESS Thomas Sicheritz-Pontn ADDRESS UPPSALA UNIVERSITY ADDRESS Biomedical Center ADDRESS Department of Molecular Biology ADDRESS BOX 590 S-751 24 UPPSALA Sweden ADDRESS BMC: +46 18 4714214 ADDRESS Fax +46 18 557723 CONTACT Thomas.Sicheritz@molbio.uu.se SITE WWW Server at URL http://evolution.bmc.uu.se/~thomas/software/grs/ OS Linux, Solaris, OFS1, IRIX LANGUAGE C++(STL), Tcl/Tk, ET, Tix VOLUME - REQUIRES - AC BC00551 NAME The Gene Discovery Page DOMAIN WWW server DOMAIN Sequence tools DOMAIN Protein sequence analysis DOMAIN Genome Analysis SERVER http://www.geocities.com/CapeCanaveral/1915/gdp.html DESCRIPTION The purpose of this page is to serve as a "desktop" area, DESCRIPTION primarily for the bench scientist with little biocomputing DESCRIPTION background. It organizes existing search engines in a DESCRIPTION coherent, stepwise fashion providing one of the many DESCRIPTION strategies that may lead to gene discovery. AUTHOR Skoufos, Emmanouil RT - ADDRESS Center for Medical Informatics ADDRESS and Section of Neurobiology ADDRESS Yale University School of Medicine ADDRESS 333 Cedar Street ADDRESS New Haven, CT 06511 CONTACT emmanouil.skoufos@yale.edu SITE WWW Server at URL http://www.geocities.com/CapeCanaveral/1915/gdp.html SITE-CONTACT - OS - LANGUAGE - VOLUME - REQUIRES - AC BC00558 NAME TEST_SHOTGUN DOMAIN Sequence analysis DOMAIN Genome Analysis DESCRIPTION TEST_SHOTGUN is a Fortran program which DESCRIPTION DESCRIPTION simulates a shotgun sequencing project. It is a handy tool DESCRIPTION for estimating not only how much work must be done (or DESCRIPTION remains to be done) for a given project, but also how much DESCRIPTION it will cost. It simulates projects up to 1 Mbp directly in DESCRIPTION memory. For projects larger than that it simulates it in 1 DESCRIPTION Mbp region and then scales the results. It is known to DESCRIPTION compile and run on OpenVMS, Digital Unix, and IRIX. DESCRIPTION Probably it will work on other platforms, or at most, DESCRIPTION require only minimal code changes. AUTHOR David Mathog RT - ADDRESS - CONTACT mathog@seqaxp.bio.caltech.edu SITE WWW Server at URL http://seqaxp.bio.caltech.edu/www/test_shotgun.html OS OpenVMS, Digital Unix, and IRIX LANGUAGE Fortran VOLUME - REQUIRES Fortran compiler AC BC00564 NAME SEALS: A System for Easy Analysis of Lots of Sequences DOMAIN Sequence format conversion tools DOMAIN Sequence tools DOMAIN Protein sequence analysis DOMAIN Pattern Identification DOMAIN Genome Analysis DOMAIN Phylogeny DOMAIN Database and analysis DOMAIN Searching databases DESCRIPTION SEALS (A System for Easy Analysis of Lots of Sequences) is a DESCRIPTION free, public domain package for large-scale sequence analysis DESCRIPTION investigations. It is still under development, but already DESCRIPTION provides a number of very useful programs, including unique DESCRIPTION taxonomy-aware tools. AUTHOR Walker DR, Koonin EV RA Walker DR, Koonin EV; RT "SEALS: A System for Easy Analysis of Lots of Sequences"; RL ISMB 5:333-339(1997). ADDRESS D Roland Walker ADDRESS National Center for Biotechnology Information ADDRESS National Library of Medicine ADDRESS National Institutes of Health, Bldg. 38A ADDRESS Bethesda, MD 20894, USA ADDRESS Voice: +1 (301)435-5909 Fax: +1 (301)435-5909 ADDRESS email: walker@ncbi.nlm.nih.gov ADDRESS ADDRESS Eugene V. Koonin, PhD ADDRESS National Center for Biotechnology Information ADDRESS National Library of Medicine ADDRESS National Institutes of Health, Bldg. 38A ADDRESS Bethesda, MD 20894, USA ADDRESS Voice: +1(301)435-5913 Fax:+1 (301)480-9241 ADDRESS email: koonin@ncbi.nlm.nih.gov CONTACT walker@ncbi.nlm.nih.gov (Roland Walker) SITE WWW Server at URL http://www.ncbi.nlm.nih.gov/Walker/SEALS/index.html OS Unix LANGUAGE Perl VOLUME 150 MB REQUIRES a number of other programs and db detailed on the home page AC BC00579 NAME Pyramids DOMAIN Protein sequence analysis DOMAIN Genome Analysis DOMAIN Phylogeny DESCRIPTION PYRAMIDS is a set of programs to create and draw a DESCRIPTION pyramidale representation of a set of sequences (given DESCRIPTION their relative distance). DESCRIPTION a pyramidal representation is a planar graph (close DESCRIPTION to upgma-like trees). DESCRIPTION DESCRIPTION one of the key feature of a pyramidal representation, DESCRIPTION is that a sequence can belong to two cluster. AUTHOR Jean-Christophe Aude. RA Aude J.C. , Diaz-Lazcoz Y. , Codani J.J. and Risler J.L.; RT "Application of the pyramidal clustering method to RT biological objects"; RL Computer & Chemistry, special issue - [accepted] ADDRESS Universite Versailles/Saint-Quentin - CGM/CNRS, FRANCE CONTACT jean-christophe.aude@inria.fr SITE WWW Server at URL http://genome.genetique.uvsq.fr/Pyramids OS SunOS, Solaris, Linux, Digital Unix, SGI Irix LANGUAGE - VOLUME 150ko REQUIRES transfig for postscript conversion (optional) COMMENTS A java application that allow you to display the pyramid COMMENTS is also available from the web site. AC BC00582 NAME TargetFinder DOMAIN Searching databases DOMAIN Pattern Identification DOMAIN Genome Analysis DOMAIN WWW server SERVER http://hercules.tigem.it/TargetFinder.html DESCRIPTION Search for target genes of transcription factors DESCRIPTION TargetFinder is a new tool to facilitate database searches DESCRIPTION for candidate target genes of transcription factors. The DESCRIPTION use of this program allows to search a database of annotated DESCRIPTION sequences for binding sites located in context with other DESCRIPTION important transcription regulatory signals and regions, DESCRIPTION like the TATA element, the transcription start site, the DESCRIPTION promoter and so on, thereby greatly reducing the background DESCRIPTION usually associated with this kind of searches. AUTHOR Giovanni Lavorgna RA Lavorgna et al. RL Trends in Genetics 14:375-376(1998). RA Lavorgna et al, 1998. RL Bioinformatics, in press ADDRESS DIBIT-HSR ADDRESS Via Olgettina, 58 ADDRESS 20132 Milano Italy CONTACT giovanni.lavorgna@hsr.it SITE WWW Server at URL http://hercules.tigem.it/TargetFinder.html OS - LANGUAGE - VOLUME - REQUIRES -