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computational gene prediction

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computational gene prediction

Postby Saneth » Tue Apr 10, 2007 10:00 am

Dear Sirs

I'm really interested in understanding the principal or theory behind the computational gene prediction softwares (especially genscan).If you have any e book or web site that I can refer pls mail to saneth.samarakoon@gmail.com
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Postby blcr11 » Tue Apr 10, 2007 9:41 pm

There is a web portal for Genescan, complete with references. You can feed your genomic sequence (up to a million bases I think) and collect the intron/exon predictions.

http://genes.mit.edu/GENSCAN.html
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Postby mith » Tue Apr 10, 2007 10:59 pm

genemark and glimmer are also two other programs
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Re: computational gene prediction

Postby ani1977 » Wed Apr 11, 2007 10:53 am

Check out the book by David Mount
Bioinformatics
Sequence and Genome Analysis, Second Edition

Welcome to the Web site that will accompany Bioinformatics: Sequence and Genome Analysis, Second Edition. The complete Web site will become available for use for the Fall semester and will be freely available to all Web users.
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Re: computational gene prediction

Postby ani1977 » Wed Apr 11, 2007 10:59 am

There is a compilations of tools at http://sharma.animesh.googlepages.com/c ... ddatabases:

FGENES and related programs that use linear discriminant analysis or hidden Markov modelsa http://genomic.sanger.ac.uk/gf/gf.shtml Solovyev et al. (1995);
GeneFinder access site at the Sanger Center http://genomic.sanger.ac.uk/gf/gf.html collection of methods
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 GeneID+b http://www1.imim.es/geneid.html Mail server at geneid@darwin.bu.edu
GeneMark and GeneMark.hmmc uses hidden Markov models http://opal.biology.gatech.edu/GeneMark/
GeneParsera,b Web page, uses combination of neural network and dynamic programming methods http://beagle.colorado.edu/~eesnyder/GeneParser.html http://beagle.colorado.edu/%7Eeesnyder/GeneParser.html Snyder and Stormo (1993, 1995)
Genescan using Fourier transform of DNA sequences to find characteristic patterns http://202.41.10.146/~sn055/DOC/gs.htm Tiwari et al. (1997)
Genetic code variations http://www.ncbi.nlm.nih.gov/htbin-post/ ... tgc?mode=c
GenLang using linguistic methods http://www.cbil.upenn.edu/ 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 (1998)
Genseqer for aligning genomic and EST sequences http://bioinformatics.iastate.edu/cgi-bin/gs.cgi Close to SplicePredictor
Glimmer uses interpolated Markov models for prokaryotic translation http://www.tigr.org/softlab/glimmer/ Salzberg et al. (1998)
GrailIIa,b prediction by neural networks based on scores of characteristic sequence patterns and composition http://compbio.ornl.gov/ Uberbacher and Mural (1991); Uberbacher et al. (1996)
Initiation codon analysis http://www.ncbi.nlm.nih.gov/htbin-post/ ... tgc?mode=c
Microbial genome coding region identification based on Markov chains of order 5 http://igs-server.cnrs-mrs.fr/~audic/selfid.html Audic and Claverie (1998)
Procrustes based on comparison of related genomic sequences http://www-hto.usc.edu/software/procrustes/ Gelfand et al. (1996)
Push-button Gene Finder for gene identification using Markov and hidden Markov models http://www.cse.ucsc.edu/research/compbio/pgf/
Translate tool at ExPASy http://www.expasy.ch/tools/dna.html
Translation machine on the Web at EBI http://www2.ebi.ac.uk/translate/
Translation of large genome sequences on the Web http://alces.med.umn.edu/rawtrans.html
Veil (Viterbi exon-intron locator) uses hidden Markov models for vertebrate DNA http://www.cs.jhu.edu/labs/compbio/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/
Webgenemark and Webgenemark.hmmc http://opal.biology.gatech.edu/GeneMark/ see GeneMark; Lukashin and Borodovsky (1998)

For a brief explanation of the well know gene-finding algorithms, check out the book by Mount [http://www.bioinformaticsonline.org/].

Basics of DNA sequence analysis is available at http://www.sildil.com/bioinformatix/gseqal.html .




Saneth wrote:Dear Sirs

I'm really interested in understanding the principal or theory behind the computational gene prediction softwares (especially genscan).If you have any e book or web site that I can refer pls mail to saneth.samarakoon_at_gmail.com
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Re:

Postby michael123 » Fri May 14, 2010 4:28 am

mith wrote:genemark and glimmer are also two other programs

Hi mith,
Are they registered versions?
and updated also?
what about other options?
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