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Nucleic Acids Research 2005 33(Web Server Issue):W465-W467; doi:10.1093/nar/gki458
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Article

AUGUSTUS: a web server for gene prediction in eukaryotes that allows user-defined constraints

Mario Stanke* and Burkhard Morgenstern

Universität Göttingen, Institut für Mikrobiologie und Genetik, Abteilung Bioinformatik Goldschmidtstraße 1, 37077 Göttingen, Germany

*To whom correspondence should be addressed. Tel: +49 551 3914926; Fax: +49 551 3914929; Email: mstanke{at}gwdg.de

Received February 14, 2005. Revised April 4, 2005. Accepted April 13, 2005.

We present a WWW server for AUGUSTUS, a software for gene prediction in eukaryotic genomic sequences that is based on a generalized hidden Markov model, a probabilistic model of a sequence and its gene structure. The web server allows the user to impose constraints on the predicted gene structure. A constraint can specify the position of a splice site, a translation initiation site or a stop codon. Furthermore, it is possible to specify the position of known exons and intervals that are known to be exonic or intronic sequence. The number of constraints is arbitrary and constraints can be combined in order to pin down larger parts of the predicted gene structure. The result then is the most likely gene structure that complies with all given user constraints, if such a gene structure exists. The specification of constraints is useful when part of the gene structure is known, e.g. by expressed sequence tag or protein sequence alignments, or if the user wants to change the default prediction. The web interface and the downloadable stand-alone program are available free of charge at http://augustus.gobics.de/submission.


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