Bioinformatics Online Home
   Chapters Links Problems Enroll for Updates Help

Home  >  Links

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 see Web site
Codon usage database see Web site
EST-GENOME for alignment of EST/cDNA and genomic sequences at MRC
see Web site; also see Florea et al. (1998)
FGENES and related programs that use linear discriminant analysis or hidden Markov models Solovyev et al. (1995); see Web site
Gene and Promoter Analysis for plants and prokaryotes see Web site
FINEX—exon–intron boundary analysis Brown et al. (1995)
GeneFinder (hexon, fgenes, Grail, and others) collection of methods see Web site
Genehacker for microbial genomes based on HMMs Hirosawa et al. (1997)
GeneID-3 Web server using rule-based models, and GeneID1 Guigó et al. (1992); Guigó (1998)
GeneMark and GeneMark.hmma uses HMMs;
Lukashin and Borodovsky (1998);
Borodovsky and McIninch (1993)
GeneParser Web page, uses combination of neural network and dynamic programming methods Snyder and Stormo (1993, 1995)
Genetic code variations
see Web site
Genie for finding human and Drosophila genes by HMMs and neural networks;
Kulp et al. (1996); Reese et al. (1997, 2000a,b)
GenLang using linguistic methods Dong and Searls (1994)
GenScan based on probabilistic model of gene structure for vertebrate, Drosophila, and plant genes Burge and Karlin (1997, 1998)
GenSeqer for aligning genomic and EST sequences see Web site and SplicePredictor
GeneSplicer for detection of splice sites based on Markov models Pertea et al. (2001)
Glimmer uses interpolated Markov models for prokaryotic translation; also GlimmerM for eukaryotes Salzberg et al. (1998)
GrailII prediction by neural networks based on scores of characteristic sequence patterns and composition Uberbacher and Mural (1991); Uberbacher et al. (1996)
Human splice sites with decision tree analysis Thanaraj (1999)
INFOGENE: a database of known gene structures and predicted genes (Commercial source) Solovyev and Salamov (1999)
MZEF uses quadratic discriminant analysis for human, mouse, Arabidopsis, and S. pombe exons Zhang (1997)
NetGene uses neural networks for analysis of splice sites in human, C. elegans, and Arabidopsis genes;;
Brunak et al. (1991); Hebsgaard et al. (1996); see NetGene
Procrustes based on comparison of related genomic sequences Gelfand et al. (1996)
SplicePredictor for plants uses trained logitlinear models Brendel and Kleffe (1998); Brendel et al. (1998)
Splicing Sites by neural network at LBNL see Genie
Translate tool at ExPASy see Web site
Translation machine on the Web at EBI see Web site
Veil (Viterbi exon–intron locator) uses HMMs for vertebrate DNA Henderson et al. (1997)
Webgene, a set of gene prediction tools and concurrent database similarity searches see Web site
Yeast splice site database by M. Ares Jr. laboratory
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.


© 2004 by Cold Spring Harbor Laboratory Press. All rights reserved.
No part of these pages, either text or image, may be used for any purpose other than personal use. Therefore, reproduction, modification, storage in a retrieval system, or retransmission, in any form or by any means, electronic, mechanical, or otherwise, for reasons other than personal use, is strictly prohibited without prior written permission.


Home Chapters Links Problems Enroll for Updates Help CSHL Press