AGenDA: gene prediction by cross-species sequence comparison

Taher L, Rinner O, Garg S, Sczyrba A, Morgenstern B (2004)
Nucleic Acids Research 32(Web Server): W305-W308.

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Abstract
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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Taher L, Rinner O, Garg S, Sczyrba A, Morgenstern B. AGenDA: gene prediction by cross-species sequence comparison. Nucleic Acids Research. 2004;32(Web Server):W305-W308.
Taher, L., Rinner, O., Garg, S., Sczyrba, A., & Morgenstern, B. (2004). AGenDA: gene prediction by cross-species sequence comparison. Nucleic Acids Research, 32(Web Server), W305-W308.
Taher, L., Rinner, O., Garg, S., Sczyrba, A., and Morgenstern, B. (2004). AGenDA: gene prediction by cross-species sequence comparison. Nucleic Acids Research 32, W305-W308.
Taher, L., et al., 2004. AGenDA: gene prediction by cross-species sequence comparison. Nucleic Acids Research, 32(Web Server), p W305-W308.
L. Taher, et al., “AGenDA: gene prediction by cross-species sequence comparison”, Nucleic Acids Research, vol. 32, 2004, pp. W305-W308.
Taher, L., Rinner, O., Garg, S., Sczyrba, A., Morgenstern, B.: AGenDA: gene prediction by cross-species sequence comparison. Nucleic Acids Research. 32, W305-W308 (2004).
Taher, L, Rinner, O, Garg, S, Sczyrba, Alexander, and Morgenstern, B. “AGenDA: gene prediction by cross-species sequence comparison”. Nucleic Acids Research 32.Web Server (2004): W305-W308.
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