AGenDA: homology-based gene prediction

Leila Taher, Oliver Rinner, Saurabh Garg, Alexander Sczyrba, Michael Brudno, Serafim Batzoglou, Burkhard Morgenstern

Research output: Contribution to journalArticleResearchpeer-review

Abstract

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.

Original languageEnglish
Pages (from-to)1575-7
Number of pages3
JournalBioinformatics
Volume19
Issue number12
DOIs
Publication statusPublished - 12 Aug 2003

Fingerprint

Homology
Genes
Gene
Genomics
Prediction
Alignment
Servers
Server
Calculate
Initiator Codon
Terminator Codon
Sequence Alignment
Graphical Representation
Electronic mail
Electronic Mail
Software System
Mouse
Exons
Software
Model

Keywords

  • Algorithms
  • Electronic Mail
  • Evolution, Molecular
  • Gene Expression Profiling/methods
  • Information Storage and Retrieval/methods
  • Internet
  • Models, Genetic
  • Phylogeny
  • Sequence Alignment/methods
  • Sequence Analysis, DNA/methods
  • Sequence Homology, Nucleic Acid
  • Software

Cite this

Taher, L., Rinner, O., Garg, S., Sczyrba, A., Brudno, M., Batzoglou, S., & Morgenstern, B. (2003). AGenDA: homology-based gene prediction. Bioinformatics, 19(12), 1575-7. https://doi.org/10.1093/bioinformatics/btg181

AGenDA : homology-based gene prediction. / Taher, Leila; Rinner, Oliver; Garg, Saurabh; Sczyrba, Alexander; Brudno, Michael; Batzoglou, Serafim; Morgenstern, Burkhard.

In: Bioinformatics, Vol. 19, No. 12, 12.08.2003, p. 1575-7.

Research output: Contribution to journalArticleResearchpeer-review

Taher, L, Rinner, O, Garg, S, Sczyrba, A, Brudno, M, Batzoglou, S & Morgenstern, B 2003, 'AGenDA: homology-based gene prediction' Bioinformatics, vol. 19, no. 12, pp. 1575-7. https://doi.org/10.1093/bioinformatics/btg181
Taher L, Rinner O, Garg S, Sczyrba A, Brudno M, Batzoglou S et al. AGenDA: homology-based gene prediction. Bioinformatics. 2003 Aug 12;19(12):1575-7. https://doi.org/10.1093/bioinformatics/btg181
Taher, Leila ; Rinner, Oliver ; Garg, Saurabh ; Sczyrba, Alexander ; Brudno, Michael ; Batzoglou, Serafim ; Morgenstern, Burkhard. / AGenDA : homology-based gene prediction. In: Bioinformatics. 2003 ; Vol. 19, No. 12. pp. 1575-7.
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