Affiliations: GSF Research Center, MIPS / Institute of
Bioinformatics, Ingolstädter Landstraße 1, 85764 Neuherberg,
Germany | Physiologisch-Chemisches Institut, Universität
Tübingen, Hoppe-Seyler-Str. 4, 72076 Tübingen, Germany | current address: Brain Research Institute, ETH Zurich,
Winterthurerstrasse 190, CH-8057 Zurich, Switzerland | current address: International Graduate School for
Bioinformatics and Genome Research, University of Bielefeld, Postfach 10 01 3,
33501 Bielefeld, Germany
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. Availability: DIALIGN is available through the
Bielefeld Bioinformatics Server (BiBiServ) at
http://bibiserv.techfak.uni-bielefeld.de/dialign/ The gene-prediction program
AGenDA described in this paper will be available through the BiBiServ or MIPS
web server at http://mips.gsf.de.
