GOPET: A tool for automated predictions of gene ontology terms

Arunachalam Vinayagam, Coral del Val, Falk Schubert, Roland Eils, Karl Heinz Glatting, Sándor Suhai, Rainer König

Research output: Contribution to journalArticle

37 Citations (Scopus)

Abstract

Background: Vast progress in sequencing projects has called for annotation on a large scale. A Number of methods have been developed to address this challenging task. These methods, however, either apply to specific subsets, or their predictions are not formalised, or they do not provide precise confidence values for their predictions. Description: We recently established a learning system for automated annotation, trained with a broad variety of different organisms to predict the standardised annotation terms from Gene Ontology (GO). Now, this method has been made available to the public via our web-service GOPET (Gene Ontology term Prediction and Evaluation Tool). It supplies annotation for sequences of any organism. For each predicted term an appropriate confidence value is provided. The basic method had been developed for predicting molecular function GO-terms. It is now expanded to predict biological process terms. This web service is available via http://genius.embnet.dkfz-heidelberg.de/menu/biounit/open-husar. Conclusion: Our web service gives experimental researchers as well as the bioinformatics community a valuable sequence annotation device. Additionally, GOPET also provides less significant annotation data which may serve as an extended discovery platform for the user.

Original languageEnglish (US)
Article number161
JournalBMC bioinformatics
Volume7
DOIs
StatePublished - Mar 20 2006

Fingerprint

Gene Ontology
Ontology
Annotation
Genes
Web services
Prediction
Evaluation
Term
Web Services
Biological Phenomena
Confidence
Bioinformatics
Computational Biology
Set theory
Learning systems
Predict
Research Personnel
Learning
Learning Systems
Equipment and Supplies

ASJC Scopus subject areas

  • Structural Biology
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Applied Mathematics

Cite this

Vinayagam, A., del Val, C., Schubert, F., Eils, R., Glatting, K. H., Suhai, S., & König, R. (2006). GOPET: A tool for automated predictions of gene ontology terms. BMC bioinformatics, 7, [161]. https://doi.org/10.1186/1471-2105-7-161

GOPET : A tool for automated predictions of gene ontology terms. / Vinayagam, Arunachalam; del Val, Coral; Schubert, Falk; Eils, Roland; Glatting, Karl Heinz; Suhai, Sándor; König, Rainer.

In: BMC bioinformatics, Vol. 7, 161, 20.03.2006.

Research output: Contribution to journalArticle

Vinayagam, A, del Val, C, Schubert, F, Eils, R, Glatting, KH, Suhai, S & König, R 2006, 'GOPET: A tool for automated predictions of gene ontology terms', BMC bioinformatics, vol. 7, 161. https://doi.org/10.1186/1471-2105-7-161
Vinayagam A, del Val C, Schubert F, Eils R, Glatting KH, Suhai S et al. GOPET: A tool for automated predictions of gene ontology terms. BMC bioinformatics. 2006 Mar 20;7. 161. https://doi.org/10.1186/1471-2105-7-161
Vinayagam, Arunachalam ; del Val, Coral ; Schubert, Falk ; Eils, Roland ; Glatting, Karl Heinz ; Suhai, Sándor ; König, Rainer. / GOPET : A tool for automated predictions of gene ontology terms. In: BMC bioinformatics. 2006 ; Vol. 7.
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