gene recognition: programs

programs (sorted alphabetically by their source)

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see also
="Banbury cross", gene identification software benchmarking (1997)=
= assessing Ab initio gene prediction methods (Sanger, 1999) =
= evaluation of gene-finding programs (Rodic of UBC and UCSC, 2001) =
= Nucleic Acids Research Web Server issue (131 web-based application programs, 2003. here is a list) =
= gene predictions on genomes (Guigo, 2002-2003) =

Univ de Barcelona, Spain (Institut Municipal de Investigacio Medica)
- GENEID: http://www1.imim.es/geneid.html (R Guigo, M Burset, JF Abril)
Beijing Genomics Institute, Beijing, China
- BGF (Beijing Genomics Institute Gene Finder) http://tlife.fudan.edu.cn/bgf/
Univ California, Berkeley, USA (Mathematics Department)
- SLAM (comparative based gene finder ) http://bio.math.berkeley.edu/slam/
Univ California, Santa Cruz, USA (Computer Science Department)
- PGF : http://www.cse.ucsc.edu/research/compbio/pgf/ (B Grundy, M Diekhans)
Celera Genomics , USA
- OTTO
Centre National de la Recherche Scientifique (CNRS), France ( Structural and Genetic Information Lab, Marseilles)
- SELFID: http://igs-server.cnrs-mrs.fr/~audic/selfid.html (S Audit, JM Claverie)
Cold Spring Harbor Lab, USA ( Zhang's lab of Computational Biology and Bioinformatics)
- MZEF: http://sciclio.cshl.org/genefinder/
- COREPROMOTER : http://sciclio.cshl.org/genefinder/CPROMOTER/
Univ of Colorado, USA (Stormo's lab, Department of Cellular and Develepmental Biology)
- GENEPARSER: http://beagle.colorado.edu/~eesnyder/GeneParser.html (E Snyder at Genomica, G Stormo)
Consiglio Nazionale delle Ricerche, Milan, Italy (Bioinformatics, Institute for Advanced Biomedical Technologies )
- WEBGENE : http://www.itba.mi.cnr.it/webgene/
  tools for prediction and analysis of protein-coding gene structure
- GENEVIEW
- GENEBUILDER
- ORFGENE
- SYNCOD
- REPEAT
- CpG
- SPLICEVIEW
- HCPOLYA
- HCTATA
European Bioinformatics Institute (Industry Support Programme)
- SpliceProximalCheck : http://industry.ebi.ac.uk/~thanaraj/SpliceProximalCheck.html
Georgia Institute of Technology, USA (Borodovsky's lab, School of Biology)
- GENEMARK: http://genemark.biology.gatech.edu/GeneMark/
- WEBGENEMARK: http://genemark.biology.gatech.edu/GeneMark/webgenemark.html
- WEBGENEMARK.HMM: http://genemark.biology.gatech.edu/GeneMark/hmmchoice.html
Genomatix Software, Neuherberg/Munich, Germany
- MATINSPECTOR (utilizes a library of matrix descriptions for transcription factor binding sites to locate matches in sequences): http://genomatix.gsf.de/products/matinspector.html
- PROMOTERINSPECTOR (highly specific prediction of promoter regions in mammalian genomic sequences): http://genomatix.gsf.de/products/PromoterInspector.html
Gesellschaft Biotechnologische Forschung (GBF), Braunschweig, Germany ( Molecular Bioinformatics of Gene Regulation Project)
- TRANSFAC-PROGRAMS (Programs used for Transcription Factor Database): http://transfac.gbf-braunschweig.de/TRANSFAC/programs.html
Univ of Gottingen, Germany ( Department of Bioinformatics )
- AUGUSTUS (predicts genes in eukaryotic genomic sequences) http://augustus.gobics.de/
Helix Research Institute, Japan ( http://www.hri.co.jp/)
- ATGpr : http://www.hri.co.jp/atgpr/
  identifying translational initiation sites in cDNA sequences
- GENIUS: http://genius.cbrc.jp/
  linking ORFs in complete genomes to protein 3D structures
Human Genome Mapping Project Resource Centre, UK ( home page )
- NIX http://www.hgmp.mrc.ac.uk/Registered/Webapp/nix/
  web tool for combining results from different programs (GRAIL, FEX, HEXON, MZEF, GENEMARK, GENEFINDER, FGENE, BLAST, POLYAH, REPEATMASKER, TRNASCAN)
Institut National de la Recherche Agronomique (INRA), Centre de Recherches de Toulouse, France (Department de Biometrie et Intelligence Artificielle)
- FRAMED http://www.toulouse.inra.fr/FrameD/cgi-bin/FD
  find genes and frameshift in G+C rich procaryotic sequences
- EUGENE http://www-bia.inra.fr/T/EuGene/
  gene finding for Arabidopsis thaliana
The Institute for Genomic Research, USA (Salzberg's lab)
- GLIMMER: http://www.tigr.org/~salzberg/glimmer.html
  finding genes in microbial DNA
- VEIL : http://www.tigr.org/~salzberg/veil.html
  hidden markov model for finding genes in vertebrate DNA
- MORGAN : http://www.tigr.org/~salzberg/morgan.html
  a decision tree system for finding genes in vertebrate DNA
Iowa State Univ., USA
- SPLICEPREDICTOR : http://gremlin1.zool.iastate.edu/cgi-bin/sp.cgi (V Brendel)
Jawaharlal Nehru Universit, India ( Nonlinearity Lab, School of Physical Sciences)
- GENESCAN: http://202.41.10.146/GS.html
  finding genes using Fourier transform
Kent Ridge Digital Labs, Singapore (Computational Immunology Group)
- Dragon Promoter Finder: http://sdmc.krdl.org.sg/promoter/
Lawrence Berkeley National Lab, USA
- GENIE: Neomorphic )
- NNPP : http://www-hgc.lbl.gov/projects/promoter.html
  promoter prediction by neural network
- NNSPLICE: http://www-hgc.lbl.gov/projects/splice.html
  splice site prediction by neural network
(Universite) Libre de Bruxelles, Belgium
- Regulatory Sequence Analysis Tools http://rsat.ulb.ac.be/rsat/ (Jacques vab Helden)
Massachusetts Institute of Technology, USA
- GENSCAN: http://genes.mit.edu/GENSCAN.html (C Burge)
- GENOMESCAN: http://genes.mit.edu/genomescan/ (C Burge)
Medical Research Council (MRC), UK (Lab of Molecular Biology)
- STADEN PACKAGE: http://www.mrc-lmb.cam.ac.uk/pubseq/index.html
Michigan Tech University, USA ( Sequence Analysis Server, Computer Science Department)
- AAT : http://genome.cs.mtu.edu/aat.html
  "Analysis and Annotation Tool", identify genes by comparing cDNA and protein sequence databases (X Huang)
- ALIGN : http://genome.cs.mtu.edu/align/align.html
  "Paiwise Sequence Alignment".
- MAP : http://genome.cs.mtu.edu/map/map.html
  "Multiple Sequence Alignment"
Univ of Minnesota, USA (Virtual Genome Center, Computational Biology Center)
- DIOGENES : http://www.cbc.umn.edu/diogenes/index.html (JA Crow)
  "a system for fast detection of coding regions in short genomic sequences"
- DNA sequence translation http://alces.med.umn.edu/webtrans.html
National Institute of Health, Japan (Department of Antibiotics)
- FRAMEPLOT: http://www.nih.go.jp/~jun/cgi-bin/frameplot.pl (J Ishikawa)
National Institute of Health, USA (Bioinformatics and Molecular Analysis Section, Center for Information Technology)
- SIGSCAN : http://bimas.dcrt.nih.gov/molbio/signal/ (D Prestridge)
National Institute of Health, USA (NCBI, National Library of Medicine )
- ORF FINDER : http://www.ncbi.nlm.nih.gov/gorf/gorf.html
- BLAST : http://www.ncbi.nlm.nih.gov/BLAST/
Oak Ridge National Lab, USA (Computational Biosciences)
- GRAIL : http://compbio.ornl.gov/Grail-bin/EmptyGrailForm
- GRAIL 1.3 : http://compbio.ornl.gov/Grail-1.3/
- XGRAIL: ftp://compbio.ornl.gov/pub/xgrail/
- GENQUEST : http://compbio.ornl.gov/Grail-bin/EmptyGenquestForm
Pasteur Institute, France ( biological software list)
- ALICE: motif discovery
- CDS : ftp://ftp.pasteur.fr/pub/GenSoft/unix/nucleic_acid/Cds/ (source)
  http://bioweb.pasteur.fr/seqanal/interfaces/cds-simple.html (online)
  search coding regions (F Chauveau)
- CDSINDEX : computer the sequence conservation across homologous sequences at each position of a multiple alignment
- FLINQS: find linker IN query sequence
- GRUPPI: clusters of binding sites
- HTML4BLAST: blast output parser
- MELTING: computer enthalpie, entripy, and melting temperature of the binding to the complementary template of an oligonucleotide
- PISE: http://www.pasteur.fr/recherche/unites/sis/Pise/ generating web interfaces for mol bio programs
Univ of Pennsylvania, USA (Computational Biology and Informatics Lab, School of Medicine)
- GENLANG : http://www.cbil.upenn.edu/~sdong/genlang_home.html
  (S Dong, DB Searl now at SmithKline)
- BIOWIDGETS: http://www.cbil.upenn.edu/bioWidgets/
- TESS : http://agave.humgen.upenn.edu/tess/index.html
Universitat Politecnica de Catalunya, Spain ( Algorithm and Genetics group , Software Department )
- PROMO : http://www.lsi.upc.es/~alggen/recerca/promo_v2/intro-promo.html (X Messeguer et al.)
Rabbithutch Biochnology Corp , Canada
- GENTERPRET:
  http://www.rabbithutch.com/
  (Gordon Hutchinson)
  SORFIND: predicting coding exons; REPFIND: identifying common repeat elements; PROMFIND prediction of promoter regions and C_pG island
Sanger Centre, UK (Computational Genomic , Informatics Division )
- Nucleotide Sequence Analysis http://genomic.sanger.ac.uk/gf/gf.html
  (V Solovyev, A Salamov)
  semi mirror site at Baylor:
  http://dot.imgen.bcm.tmc.edu:9331/gene-finder/gf.html
- Protein Sequence Analysis http://genomic.sanger.ac.uk/pss/pss.html
- 3-D Structure Analysis http://genomic.sanger.ac.uk/123D/123D.html
- TAAFGI : http://genomic.sanger.ac.uk/db.html
  Tools for Analysis and Annotation of Functional Genome Information
Softberry, Inc. USA/Russia ( home page)
- FGENES : http://www.softberry.com/berry.phtml?topic=index&group=programs&subgroup=gfind (gene models construction, splice sites, protein-coding exons) (-H: hidden Markov model, -B:bacterial; -V: viral)
- promoter search : http://www.softberry.com/berry.phtml?topic=promoter
Univ of Southern California, USA ( Center for Computational and Experimental Genommics)
- PROCRUSTES: http://www-hto.usc.edu/software/procrustes/index.html
- ALIGNMENT : http://www-hto.usc.edu/software/seqaln/seqaln-query.html
Technical University of Denmark, Denmark (Center for Biological Sequence Analysis, Department of Biotechnology)
- HMMGENE: http://www.cbs.dtu.dk/services/HMMgene/
  prediction of vertebrate and c. elegans genes
- NETGENE2: http://www.cbs.dtu.dk/services/NetGene2/
  intron splice site prediction in human c. elegans, a. thaliana
- NETPLANTGENE: http://www.cbs.dtu.dk/services/NetPGene/
  intron splice site prediction in a. thaliana DNA
- NETSTART: http://www.cbs.dtu.dk/services/NetStart/
  translation start in vertebrate and a. thaliana DNA
- PROMOTER : http://www.cbs.dtu.dk/services/promoter/
- RNA strcuture logos : http://www.cbs.dtu.dk/gorodkin/appl/slogo.html
TianJin University , China ( Center of Bioinformatics)
- GS-FINDER: http://tubic.tju.edu.cn/GS-Finder/
  finding bacterial gene start sites with a self-training method
- YEASTGENE : http://tubic.tju.edu.cn/cgi-bin/Yeastgene.cgi
  measure the coding ability of an ORF or a fragment of DNA sequence in Saccharomyces cerevisiae genome.
- ZCURVE : http://tubic.tju.edu.cn/Zcurve_B/
  recognizing protein coding genes in bacterial and archaeal genomes.
Univ of Washington ( Genome Center)
- GENEFINGER (Phil Green, phg@u.washington.edu)