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GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses
1School of Biology, Georgia Institute of Technology Atlanta, GA 30332, USA 2Department of Biomedical Engineering, Georgia Institute of Technology Atlanta, GA 30332, USA
*To whom correspondence should be addressed. Tel: +1 404 894 8432; Fax: +1 404 894 0519; Email: mark.borodovsky{at}biology.gatech.edu
Received February 14, 2005. Revised April 20, 2005. Accepted April 20, 2005.
The task of gene identification frequently confronting researchers working with both novel and well studied genomes can be conveniently and reliably solved with the help of the GeneMark web software (http://opal.biology.gatech.edu/GeneMark/). The website provides interfaces to the GeneMark family of programs designed and tuned for gene prediction in prokaryotic, eukaryotic and viral genomic sequences. Currently, the server allows the analysis of nearly 200 prokaryotic and >10 eukaryotic genomes using species-specific versions of the software and pre-computed gene models. In addition, genes in prokaryotic sequences from novel genomes can be identified using models derived on the spot upon sequence submission, either by a relatively simple heuristic approach or by the full-fledged self-training program GeneMarkS. A database of reannotations of >1000 viral genomes by the GeneMarkS program is also available from the web site. The GeneMark website is frequently updated to provide the latest versions of the software and gene models.
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