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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.

 

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