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. 2005 Jul 1;33(Web Server issue):W451-4.
doi: 10.1093/nar/gki487.

GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses

John Besemer  1 , Mark Borodovsky
Affiliations

GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses

John Besemer et al. Nucleic Acids Res. .

Abstract

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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Figures

Figure 1
Figure 1
Graphical output from the combination of GeneMark and GeneMark.hmm for a fragment of the Escherichia coli K12 genome. The solid black and dashed traces indicate the coding potential calculated by the GeneMark program using the Typical and Atypical Markov chain models of coding DNA, respectively. Only the three reading frames in the direct strand are shown as there are no genes (either predicted or annotated) on the reverse strand in this section of the genome. The thick black horizontal bars indicate the locations of the predictions made by GeneMark.hmm. The thick grey horizontal bars indicate ‘regions of interest’ provided by the GeneMark program. The thin black horizontal lines indicate (longest) ORFs observed in each reading frame; ticks extending above and below this line indicate potential start and stop codons, respectively.
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