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Nucleic Acids Research 2006 34(Web Server issue):W10-W14; doi:10.1093/nar/gkl330
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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

FISH—family identification of sequence homologues using structure anchored hidden Markov models

Jeanette Tångrot1,2, Lixiao Wang1, Bo Kågström2,3 and Uwe H. Sauer1,*

1 Umeå Center for Molecular Pathogenesis UCMP 2 Department of Computing Science, HPC2N, Umeå University Umeå, Sweden 3 High Performance Computing Center North, HPC2N, Umeå University Umeå, Sweden

*To whom correspondence should be addressed. Tel: +46 90 785 6784; Fax: +46 90 77 80 07; Email: uwe{at}ucmp.umu.se

Received February 14, 2006. Revised March 1, 2006. Accepted April 14, 2006.

The FISH server is highly accurate in identifying the family membership of domains in a query protein sequence, even in the case of very low sequence identities to known homologues. A performance test using SCOP sequences and an E-value cut-off of 0.1 showed that 99.3% of the top hits are to the correct family saHMM. Matches to a query sequence provide the user not only with an annotation of the identified domains and hence a hint to their function, but also with probable 2D and 3D structures, as well as with pairwise and multiple sequence alignments to homologues with low sequence identity. In addition, the FISH server allows users to upload and search their own protein sequence collection or to quarry public protein sequence data bases with individual saHMMs. The FISH server can be accessed at http://babel.ucmp.umu.se/fish/.


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