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Nucleic Acids Research 2006 34(Web Server issue):W214-W218; doi:10.1093/nar/gkl332
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© The Author 2006. Published by Oxford University Press. All rights reserved
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, please contact journals.permissions@oxfordjournals.org

Article

DOUTfinder—identification of distant domain outliers using subsignificant sequence similarity

Maria Novatchkova1,*, Georg Schneider1, Richard Fritz2, Frank Eisenhaber1 and Alexander Schleiffer1

1 Research Institute of Molecular Pathology (IMP), Dr Bohr-Gasse 7 A-1030 Vienna, Austria 2 Institute of Virology, Medical University of Vienna Kinderspitalgasse 15, A-1095 Vienna, Austria

*To whom correspondence should be addressed. Tel: +43 1 7973 0556; Fax: +43 1 7987 153; Email: novatchkova{at}imp.univie.ac.at

Received February 15, 2006. Revised March 4, 2006. Accepted April 14, 2006.

DOUTfinder is a web-based tool facilitating protein domain detection among related protein sequences in the twilight zone of sequence similarity. The sequence set required for this analysis can be provided by the user or will be collected using PSI-BLAST if a single sequence is given as an input. The obtained sequence family is analyzed for known Pfam and SMART domains, and the thereby identified subsignificant domain similarities are evaluated further. Domains with several subthreshold hits in the query set are ranked based on a sum-score function and likely homologous domains are suggested according to established cut-offs. By providing a post-filtering procedure for subsignificant domain hits DOUTfinder allows the detection of non-trivial domain relationships and can thereby lead to new insights into the function and evolution of distantly related sequence families. DOUTfinder is available at http://mendel.imp.ac.at/dout/.


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