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PubMed · 12542405

AGenDA: gene prediction by comparative sequence analysis.

Oliver Rinner·Burkhard Morgenstern
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Abstract

UNLABELLED: 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.

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AlgorithmsAnimalsExonsHumansMiceSequence AnalysisComparative StudyJournal ArticleResearch Support, Non-U.S. Gov't

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Oliver Rinner, Burkhard Morgenstern. 2002. AGenDA: gene prediction by comparative sequence analysis.. https://pubmed.ncbi.nlm.nih.gov/12542405/

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