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computational gene prediction

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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.
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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
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 ... ddatabases:

FGENES and related programs that use linear discriminant analysis or hidden Markov modelsa Solovyev et al. (1995);
GeneFinder access site at the Sanger Center collection of methods
Genehacker for microbial genomes based on HMMs Hirosawa et al. (1997)
GeneID-3 Web server using rule-based models, and GeneID+b Mail server at [email protected]
GeneMark and GeneMark.hmmc uses hidden Markov models
GeneParsera,b Web page, uses combination of neural network and dynamic programming methods Snyder and Stormo (1993, 1995)
Genescan using Fourier transform of DNA sequences to find characteristic patterns Tiwari et al. (1997)
Genetic code variations ... tgc?mode=c
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 (1998)
Genseqer for aligning genomic and EST sequences Close to SplicePredictor
Glimmer uses interpolated Markov models for prokaryotic translation Salzberg et al. (1998)
GrailIIa,b prediction by neural networks based on scores of characteristic sequence patterns and composition Uberbacher and Mural (1991); Uberbacher et al. (1996)
Initiation codon analysis ... tgc?mode=c
Microbial genome coding region identification based on Markov chains of order 5 Audic and Claverie (1998)
Procrustes based on comparison of related genomic sequences Gelfand et al. (1996)
Push-button Gene Finder for gene identification using Markov and hidden Markov models
Translate tool at ExPASy
Translation machine on the Web at EBI
Translation of large genome sequences on the Web
Veil (Viterbi exon-intron locator) uses hidden Markov models for vertebrate DNA Henderson et al. (1997)
Webgene, a set of gene prediction tools and concurrent database similarity searches
Webgenemark and Webgenemark.hmmc see GeneMark; Lukashin and Borodovsky (1998)

For a brief explanation of the well know gene-finding algorithms, check out the book by Mount [].

Basics of DNA sequence analysis is available at .

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
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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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