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RECOMB Workshop on Comparative Genomics

RCG 2005: Comparative Genomics pp 61–72Cite as

OMA, A Comprehensive, Automated Project for the Identification of Orthologs from Complete Genome Data: Introduction and First Achievements

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Part of the Lecture Notes in Computer Science book series (LNBI,volume 3678)

Abstract

The OMA project is a large-scale effort to identify groups of orthologs from complete genome data, currently 150 species. The algorithm relies solely on protein sequence information and does not require any human supervision. It has several original features, in particular a verification step that detects paralogs and prevents them from being clustered together. Consistency checks and verification are performed throughout the process. The resulting groups, whenever a comparison could be made, are highly consistent both with EC assignments, and with assignments from the manually curated database HAMAP. A highly accurate set of orthologous sequences constitutes the basis for several other investigations, including phylogenetic analysis and protein classification.

Keywords

  • Vertex Cover
  • Maximal Clique
  • Lateral Gene Transfer
  • Orthologous Relationship
  • Multidomain Protein

These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Author information

Authors and Affiliations

  1. Institute of Computational Science, ETH Zurich, CH-8092, Zürich

    Christophe Dessimoz, Gina Cannarozzi, Manuel Gil, Daniel Margadant, Alexander Roth, Adrian Schneider & Gaston H. Gonnet

Authors
  1. Christophe Dessimoz
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  2. Gina Cannarozzi
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  3. Manuel Gil
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  4. Daniel Margadant
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  5. Alexander Roth
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  6. Adrian Schneider
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  7. Gaston H. Gonnet
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Editor information

Editors and Affiliations

  1. University of Dublin, Smurfit Institute of Genetics, Trinity College, Ireland

    Aoife McLysaght

  2. Center for Bioinformatics ZBIT, Tübingen University, Sand 14, 72076, Tübingen, Germany

    Daniel H. Huson

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© 2005 Springer-Verlag Berlin Heidelberg

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Dessimoz, C. et al. (2005). OMA, A Comprehensive, Automated Project for the Identification of Orthologs from Complete Genome Data: Introduction and First Achievements. In: McLysaght, A., Huson, D.H. (eds) Comparative Genomics. RCG 2005. Lecture Notes in Computer Science(), vol 3678. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11554714_6

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  • DOI: https://doi.org/10.1007/11554714_6

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-28932-6

  • Online ISBN: 978-3-540-31814-9

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