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Nucleic Acids Research 2005 33(Database Issue):D188-D191; doi:10.1093/nar/gki096
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Nucleic Acids Research, 2005, Vol. 33, Database issue D188-D191
© 2005, the authors
Nucleic Acids Research, Vol. 33, Database issue © Oxford University Press 2005; all rights reserved

ADDA: a domain database with global coverage of the protein universe

Andreas Heger1,*, Christopher Andrew Wilton1, Ashwin Sivakumar1 and Liisa Holm1,2

1 Institute of Biotechnology, and 2 Department of Genetics, University of Helsinki, 00014 Helsinki, Finland

* To whom correspondence should be addressed. Tel: +358 9 191 59115; Fax: +358 9 191 59366; Email: andreas.heger{at}helsinki.fi
Correspondence may be addressed to Liisa Holm. Email: liisa.holm{at}helsinki.fi

Received August 16, 2004; Revised and Accepted October 13, 2004

We used the Automatic Domain Decomposition Algorithm (ADDA) to generate a database of protein domain families with complete coverage of all protein sequences. Sequences are split into domains and domains are grouped into protein domain families in a completely automated process. The current database contains domains for more than 1.5 million sequences in more than 40 000 domain families. In particular, there are 3828 novel domain families that do not overlap with the curated domain databases Pfam, SCOP and InterPro. The data are freely available for downloading and querying via a web interface (http://ekhidna.biocenter.helsinki.fi:9801/sqgraph/pairsdb).

The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use permissions, please contact journals.permissions{at}oupjournals.org.


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