© 2006 The Author(s)
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AUGUSTUS: ab initio prediction of alternative transcripts
Institut für Mikrobiologie und Genetik, Abteilung Bioinformatik Goldschmidtstrasse 1, 37077 Göttingen, Germany 1 Institut für Informatik, Lotzestrasse 16-18 37083 Göttingen, Germany 2 Philip Morris USA, Research Center Richmond, VA 23261, USA
*To whom correspondence should be addressed. Tel: +1 831 459 5232; Fax: +1 832 459 1809; Email: mstanke{at}gwdg.de
Received February 14, 2006. Revised March 21, 2006. Accepted March 21, 2006.
AUGUSTUS is a software tool for gene prediction in eukaryotes based on a Generalized Hidden Markov Model, a probabilistic model of a sequence and its gene structure. Like most existing gene finders, the first version of AUGUSTUS returned one transcript per predicted gene and ignored the phenomenon of alternative splicing. Herein, we present a WWW server for an extended version of AUGUSTUS that is able to predict multiple splice variants. To our knowledge, this is the first ab initio gene finder that can predict multiple transcripts. In addition, we offer a motif searching facility, where user-defined regular expressions can be searched against putative proteins encoded by the predicted genes. The AUGUSTUS web interface and the downloadable open-source stand-alone program are freely available from http://augustus.gobics.de.
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