AGenDA: homology-based gene prediction

Taher L, Rinner O, Garg S, Sczyrba A, Brudno M, Batzoglou S, Morgenstern B (2003)
BIOINFORMATICS 19(12): 1575-1577.

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We present a www server for homology-based gene prediction. The user enters a pair of evolutionary related genomic sequences, for example from human and mouse. Our software system uses CHAOS and DIALIGN to calculate an alignment of the input sequences and then searches for conserved splicing signals and start/stop codons around regions of local sequence similarity. This way, candidate exons are identified that are used, in turn, to calculate optimal gene models. The server returns the constructed gene model by email, together with a graphical representation of the underlying genomic alignment.
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Taher L, Rinner O, Garg S, et al. AGenDA: homology-based gene prediction. BIOINFORMATICS. 2003;19(12):1575-1577.
Taher, L., Rinner, O., Garg, S., Sczyrba, A., Brudno, M., Batzoglou, S., & Morgenstern, B. (2003). AGenDA: homology-based gene prediction. BIOINFORMATICS, 19(12), 1575-1577.
Taher, L., Rinner, O., Garg, S., Sczyrba, A., Brudno, M., Batzoglou, S., and Morgenstern, B. (2003). AGenDA: homology-based gene prediction. BIOINFORMATICS 19, 1575-1577.
Taher, L., et al., 2003. AGenDA: homology-based gene prediction. BIOINFORMATICS, 19(12), p 1575-1577.
L. Taher, et al., “AGenDA: homology-based gene prediction”, BIOINFORMATICS, vol. 19, 2003, pp. 1575-1577.
Taher, L., Rinner, O., Garg, S., Sczyrba, A., Brudno, M., Batzoglou, S., Morgenstern, B.: AGenDA: homology-based gene prediction. BIOINFORMATICS. 19, 1575-1577 (2003).
Taher, L, Rinner, O, Garg, S, Sczyrba, Alexander, Brudno, M, Batzoglou, S, and Morgenstern, B. “AGenDA: homology-based gene prediction”. BIOINFORMATICS 19.12 (2003): 1575-1577.
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8 Citations in Europe PMC

Data provided by Europe PubMed Central.

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Multiple alignment of genomic sequences using CHAOS, DIALIGN and ABC.
Pohler D, Werner N, Steinkamp R, Morgenstern B., Nucleic Acids Res. 33(Web Server issue), 2005
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AGenDA: gene prediction by cross-species sequence comparison.
Taher L, Rinner O, Garg S, Sczyrba A, Morgenstern B., Nucleic Acids Res. 32(Web Server issue), 2004
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The CHAOS/DIALIGN WWW server for multiple alignment of genomic sequences.
Brudno M, Steinkamp R, Morgenstern B., Nucleic Acids Res. 32(Web Server issue), 2004
PMID: 15215346
Fast and sensitive multiple alignment of large genomic sequences.
Brudno M, Chapman M, Gottgens B, Batzoglou S, Morgenstern B., BMC Bioinformatics 4(), 2003
PMID: 14693042

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