- Article -
| In Silico Biology 2, 0018 (2002); ©2002, Bioinformation Systems e.V. |
AGenDA: Gene prediction by comparative sequence analysis
Oliver Rinner1,2,3 and Burkhard Morgenstern1,4
1GSF Research Center, MIPS / Institute of Bioinformatics, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
2Physiologisch-Chemisches Institut, Universität Tübingen, Hoppe-Seyler-Str. 4, 72076 Tübingen, Germany
3current address: Brain Research Institute, ETH Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
4current address: International Graduate School for Bioinformatics and Genome Research, University of Bielefeld, Postfach 100131, 33501 Bielefeld, Germany
Edited by E. Wingender; received November 30, 2001; revised and accepted January 7, 2002; published March 15, 2002
Abstract
Comparative sequence analysis is a powerful approach to identify functional elements in genomic sequences. Herein, we describe AGenDA (Alignment-based GENe Detection Algorithm), a novel method for gene prediction that is based on long-range alignment of syntenic regions in eukaryotic genome sequences. Local sequence homologies identified by the DIALIGN program are searched for conserved splice signals to define potential protein-coding exons; these candidate exons are then used to assemble complete gene structures. The performance of our method was tested on a set of 105 human-mouse sequence pairs. These test runs showed that sensitivity and specificity of AGenDA are comparable with the best gene- prediction program that is currently available. However, since our method is based on a completely different type of input information, it can detect genes that are not detectable by standard methods and vice versa. Thus, our approach seems to be a useful addition to existing gene-prediction programs.
Keywords: gene prediction, sequence alignment, comparative genome analysis, cross-species sequence comparison, phylogenetic footprinting, genome annotation, dynamic programming