Table 9.1. Programs and Web pages for sequence translation and related information |
Name of translation site |
|
Web address |
|
Reference |
|
Arabidopis intron splice site table |
http://www.nal.usda.gov/pgdic/Probe/v2n3/codon.html |
see Web site |
Codon usage database |
http://www.kazusa.or.jp/codon/ |
see Web site |
EST-GENOME for alignment of EST/cDNA and genomic sequences at MRC |
http://www.hgmp.mrc.ac.uk/Registered/Option/
est_genome.html |
see Web site; also see Florea et al. (1998) |
FGENES and related programs that use linear discriminant analysis or hidden Markov models |
http://searchlauncher.bcm.tmc.edu/seq-search/gene-search.html |
Solovyev et al. (1995); see Web site |
Gene and Promoter Analysis for plants and prokaryotes |
http://mendel.cs.rhul.ac.uk/mendel.php |
see Web site |
FINEX—exon–intron boundary analysis |
http://www.sanger.ac.uk/cgi-bin/finex/finex_search.pl |
Brown et al. (1995) |
GeneFinder (hexon, fgenes, Grail, and others) collection of methods |
http://searchlauncher.bcm.tmc.edu/seq-search/gene-search.html |
see Web site |
Genehacker for microbial genomes based on HMMs |
http://www-btls.jst.go.jp/GeneHacker/ |
Hirosawa et al. (1997) |
GeneID-3 Web server using rule-based models, and GeneID1 |
http://www1.imim.es/geneid.html |
Guigó et al. (1992); Guigó (1998) |
GeneMark and GeneMark.hmma uses HMMs |
http://opal.biology.gatech.edu/GeneMark/;
http://www2.ebi.ac.uk/genemark/ |
Lukashin and Borodovsky (1998); Borodovsky and McIninch (1993) |
GeneParser Web page, uses combination of neural network and dynamic programming methods |
http://obesitygene.pbrc.edu/~eesnyder/geneparser.htm |
Snyder and Stormo (1993, 1995) |
Genetic code variations |
http://www.ncbi.nlm.nih.gov/
Taxonomy/taxonomyhome.html |
see Web site |
Genie for finding human and Drosophila genes by HMMs and neural networks |
http://www.cse.ucsc.edu/~dkulp/cgi-bin/genie;
http://www.fruitfly.org/seq_tools/genie.html
|
Kulp et al. (1996); Reese et al. (1997, 2000a,b) |
GenLang using linguistic methods |
http://www.cbil.upenn.edu/genlang/genlang.html |
Dong and Searls (1994) |
GenScan based on probabilistic model of gene structure for vertebrate, Drosophila, and plant genes |
http://genes.mit.edu/GENSCAN.html |
Burge and Karlin (1997, 1998) |
GenSeqer for aligning genomic and EST sequences |
http://bioinformatics.iastate.edu/cgi-bin/gs.cgi |
see Web site and SplicePredictor |
GeneSplicer for detection of splice sites based on Markov models |
http://www.tigr.org/software/ |
Pertea et al. (2001) |
Glimmer uses interpolated Markov models for prokaryotic translation; also GlimmerM for eukaryotes |
http://www.tigr.org/software/ |
Salzberg et al. (1998) |
GrailII prediction by neural networks based on scores of characteristic sequence patterns and composition |
http://compbio.ornl.gov/public/tools/ |
Uberbacher and Mural (1991); Uberbacher et al. (1996) |
Human splice sites with decision tree analysis |
http://industry.ebi.ac.uk/~thanaraj/splice.html |
Thanaraj (1999) |
INFOGENE: a database of known gene structures and predicted genes |
http://genomic.sanger.ac.uk/inf/infodb.shtml (Commercial source) |
Solovyev and Salamov (1999) |
MZEF uses quadratic discriminant analysis for human, mouse, Arabidopsis, and S. pombe exons |
http://rulai.cshl.edu/ |
Zhang (1997) |
NetGene uses neural networks for analysis of splice sites in human, C. elegans, and Arabidopsis genes |
http://www.cbs.dtu.dk/services/NetGene2/;
http://www.cbs.dtu.dk/services/NetPGene/;
http://www.cbs.dtu.dk/services/NetStart/ |
Brunak et al. (1991); Hebsgaard et al. (1996); see NetGene |
Procrustes based on comparison of related genomic sequences |
http://hto-13.usc.edu/software/procrustes/index.html |
Gelfand et al. (1996) |
SplicePredictor for plants uses trained logitlinear models |
http://bioinformatics.iastate.edu/cgi-bin/sp.cgi |
Brendel and Kleffe (1998); Brendel et al. (1998) |
Splicing Sites by neural network at LBNL |
http://www.fruitfly.org/seq_tools/splice.html |
see Genie |
Translate tool at ExPASy |
http://www.expasy.org/tools/dna.html |
see Web site |
Translation machine on the Web at EBI |
http://www2.ebi.ac.uk/translate/ |
see Web site |
Veil (Viterbi exon–intron locator) uses HMMs for vertebrate DNA |
http://www.tigr.org/~salzberg/veil.html |
Henderson et al. (1997) |
Webgene, a set of gene prediction tools and concurrent database similarity searches |
http://www.itba.mi.cnr.it/webgene/ |
see Web site |
Yeast splice site database by M. Ares Jr. laboratory |
http://www.cse.ucsc.edu/research/compbio/
yeast_introns.html |
Spingola et al. (1999) |
|
Abbreviations: (LBNL) Lawrence Berkeley National Laboratory, (EBI) European Bioinformatics Institute.
a The GeneMark.hmm program is designed to use additional information at the 5' end of bacterial sequences.
|