AGenDA: gene prediction by cross-species sequence comparison
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 Brain Research Institute, ETH Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland, 4 Faculty of Technology, Research Group in Practical Computer Science, University of Bielefeld, Postfach 10 01 31, 33501 Bielefeld, Germany and 5 Institute of Microbiology and Genetics, University of Göttingen, Goldschmidtstrasse 1, 37077 Göttingen, Germany
* To whom correspondence should be addressed. Tel: +49 551 39 14628; Fax: +49 551 39 14929; Email: bmorgen{at}gwdg.de
Received March 5, 2004; Revised and Accepted March 24, 2004
Automatic gene prediction is one of the major challenges in computational sequence analysis. Traditional approaches to gene finding rely on statistical models derived from previously known genes. By contrast, a new class of comparative methods relies on comparing genomic sequences from evolutionary related organisms to each other. These methods are based on the concept of phylogenetic footprinting: they exploit the fact that functionally important regions in genomic sequences are usually more conserved than non-functional regions. We created a WWW-based software program for homology-based gene prediction at BiBiServ (Bielefeld Bioinformatics Server). Our tool takes pairs of evolutionary related genomic sequences as input data, e.g. from human and mouse. The server runs CHAOS and DIALIGN to create an alignment of the input sequences and subsequently searches for conserved splicing signals and start/stop codons near regions of local sequence conservation. Genes are predicted based on local homology information and splice signals. The server returns predicted genes together with a graphical representation of the underlying alignment. The program is available at http://bibiserv.TechFak.Uni-Bielefeld.DE/agenda/.
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