AGenDA: homology-based gene prediction

Taher, L; Rinner, O; Garg, S; Sczyrba, Alexander; Brudno, M; Batzoglou, S; Morgenstern, B

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.

Zeitschriftenaufsatz | Veröffentlicht | Englisch

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DOI

https://doi.org/10.1093/bioinformatics/btg181

Autor*in

Taher, L; Rinner, O; Garg, S; Sczyrba, Alexander^UniBi ; Brudno, M; Batzoglou, S; Morgenstern, B

Einrichtung

Technische Fakultät > Computational Metagenomics
Centrum für Biotechnologie > Arbeitsgruppe A. Sczyrba
Centrum für Biotechnologie > Graduate Center
Centrum für Biotechnologie > Technologieplattformen > Bielefeld University Bioinformatics Services

Abstract / Bemerkung

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.

Erscheinungsjahr

2003

Zeitschriftentitel

BIOINFORMATICS

Band

Ausgabe

Seite(n)

1575-1577

ISSN

1367-4803

eISSN

1460-2059

Page URI

https://pub.uni-bielefeld.de/record/1610494

Zitieren

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. https://doi.org/10.1093/bioinformatics/btg181

Taher, L, Rinner, O, Garg, S, Sczyrba, Alexander, Brudno, M, Batzoglou, S, and 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.

Daten bereitgestellt von European Bioinformatics Institute (EBI)

9 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

Combining gene prediction methods to improve metagenomic gene annotation.
Yok NG, Rosen GL., BMC Bioinformatics 12(), 2011
PMID: 21232129

DIALIGN-TX: greedy and progressive approaches for segment-based multiple sequence alignment.
Subramanian AR, Kaufmann M, Morgenstern B., Algorithms Mol Biol 3(), 2008
PMID: 18505568

Comparative genomics of small RNAs in bacterial genomes.
Luban S, Kihara D., OMICS 11(1), 2007
PMID: 17411396

Vertebrate gene finding from multiple-species alignments using a two-level strategy.
Carter D, Durbin R., Genome Biol 7 Suppl 1(), 2006
PMID: 16925840

Multiple alignment of genomic sequences using CHAOS, DIALIGN and ABC.
Pöhler D, Werner N, Steinkamp R, Morgenstern B., Nucleic Acids Res 33(web server issue), 2005
PMID: 15980528

Comparative genomics: methods and applications.
Haubold B, Wiehe T., Naturwissenschaften 91(9), 2004
PMID: 15278216

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

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
PMID: 15215399

Fast and sensitive multiple alignment of large genomic sequences.
Brudno M, Chapman M, Göttgens B, Batzoglou S, Morgenstern B., BMC Bioinformatics 4(), 2003
PMID: 14693042