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Bioinformatics Vol. 19 no. 12 2003
Pages 1575-1577
© 2003 Oxford University Press

Applications Note

AGenDA: homology-based gene prediction

Leila Taher 1,*, Oliver Rinner 2, Saurabh Garg 1, Alexander Sczyrba 3, Michael Brudno 4, Serafim Batzoglou 4 and Burkhard Morgenstern 1,5

1 International Graduate School for Bioinformatics and Genome Research University of Bielefeld, Postfach 10 01 31, 33501 Bielefeld, Germany
2 GSF Research Center, MIPS / Institute of Bioinformatics, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
3 Faculty of Technology, Research Group in Practical Computer Science, University of Bielefeld, Postfach 10 01 31, 33501 Bielefeld, Germany
4 Computer Science Department, Stanford University, Stanford, CA 94305, USA
5 University of Göttingen, Institute of Microbiology and Genetics, Goldschmidtstr. 1, 37077 Göttingen, Germany

Received on August 19, 2002 ; revised on November 30, 2002 ; accepted on February 14, 2002

Summary: We present a www server for homology-based gene prediction. The user enters a pair of evolutionary related genomic sequences, for example from human and mouse. Our software system uses CHAOS and DIALIGN to calculate an alignment of the input sequences and then searches for conserved splicing signals and start/stop codons around regions of local sequence similarity. This way, candidate exons are identified that are used, in turn, to calculate optimal gene models. The server returns the constructed gene model by email, together with a graphical representation of the underlying genomic alignment.

Availability: http://bibiserv.TechFak.Uni-Bielefeld.DE/agenda/

Contact: ltaher{at}TechFak.Uni-Bielefeld.DE

* To whom correspondence should be addressed.


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