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Bioinformatics Advance Access originally published online on August 31, 2009
Bioinformatics 2009 25(22):3020-3025; doi:10.1093/bioinformatics/btp522
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© The Author 2009. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Comparative analysis and unification of domain–domain interaction networks

Patrik Björkholm * and Erik L. L. Sonnhammer

Stockholm Bioinformatics Center, Albanova, Stockholm University, 10691 Stockholm, Sweden

*To whom correspondence should be addressed.


  Abstract

Motivation: Certain protein domains are known to preferentially interact with other domains. Several approaches have been proposed to predict domain–domain interactions, and over nine datasets are available. Our aim is to analyse the coverage and quality of the existing resources, as well as the extent of their overlap. With this knowledge, we have the opportunity to merge individual domain interaction networks to construct a comprehensive and reliable database.

Results: In this article we introduce a new approach towards comparing domain–domain interaction networks. This approach is used to compare nine predicted domain and protein interaction networks. The networks were used to generate a database of unified domain interactions, UniDomInt. Each interaction in the dataset is scored according to the benchmarked reliability of the sources. The performance of UniDomInt is an improvement compared to the underlying source networks and to another composite resource, Domine.

Availability: http://sonnhammer.sbc.su.se/download/UniDomInt/

Contact: Erik.Sonnhammer{at}sbc.su.se

Associate Editor: Dmitrij Frishman

Received on May 4, 2009; revised on August 12, 2009; accepted on August 26, 2009

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