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Nucleic Acids Research 2004 32(Web Server Issue):W309-W312; doi:10.1093/nar/gkh379
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© 2004, the authors
Nucleic Acids Research, Vol. 32, Web Server issue © Oxford University Press 2004; all rights reserved

AUGUSTUS: a web server for gene finding in eukaryotes

Mario Stanke*, Rasmus Steinkamp, Stephan Waack1 and Burkhard Morgenstern

University of Göttingen, Institut für Mikrobiologie und Genetik, Goldschmidtstraße 1, 37077 Göttingen, Germany and 1 University of Göttingen, Institut für Numerische und Angewandte Mathematik, Lotzestraße 16–18, 37083 Göttingen, Germany

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

Received February 14, 2004; Revised and Accepted March 15, 2004

We present a www server for AUGUSTUS, a novel software program for ab initio gene prediction in eukaryotic genomic sequences. Our method is based on a generalized Hidden Markov Model with a new method for modeling the intron length distribution. This method allows approximation of the true intron length distribution more accurately than do existing programs. For genomic sequence data from human and Drosophila melanogaster, the accuracy of AUGUSTUS is superior to existing gene-finding approaches. The advantage of our program becomes apparent especially for larger input sequences containing more than one gene. The server is available at http://augustus.gobics.de.

The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated.


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