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Bioinformatics Advance Access published online on May 5, 2007
Bioinformatics, doi:10.1093/bioinformatics/btm240
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© The Author (2007). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Automated Improvement of Domain ANnotations using context analysis of Domain Arrangements (AIDAN)

Francois Beaussart , January Weiner, 3rd and Erich Bornberg-Bauer

Evolutionary Bioinformatics, Institute for Evolution and Biodiversity, Westfälische Wilhelms University, Schlossplatz 4, D48149 Münster, Germany

To whom correspondence should be addressed. Prof. Erich Bornberg-Bauer, E-mail: ebb{at}uni-muenster.de


  Abstract

Motivation: Since protein domains are the units of evolution, databases of domain signatures such as ProDom or Pfam enable both a sensitive and selective sequence analysis. However, manually curated databases have a low coverage and automatically generated ones often miss relationships which have not yet been discovered between domains or cannot display similarities between domains which have drifted apart

Methods: We present a tool which makes use of the fact that overall domain arrangements are often conserved. AIDAN (Automated Improvement of Domain ANnotations) identifies potential annotation artifacts and domains which have drifted apart. The underlying database supplements ProDom and is interfaced by a graphical tool allowing the localization of single domain deletions or annotations which have been falsely made by the automated procedure.

Availability: http://www.uni-muenster.de/evolution/ebb/Services/AIDAN http://www.uni-muenster.de/Evolution.ebb/Publications/pdf_free/beaussartebb-aidan-bioinformatics-submitted-2006-supplementary-material.pdf

Associate Editor: Prof. Dmitrij Frishman

Received on December 8, 2006; revised on April 18, 2007; accepted on April 27, 2007

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