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Nucleic Acids Research 2006 34(Web Server issue):W374-W378; doi:10.1093/nar/gkl195
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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

HHsenser: exhaustive transitive profile search using HMM–HMM comparison

Johannes Söding*, Michael Remmert, Andreas Biegert and Andrei N. Lupas

Department of Protein Evolution, Max-Planck-Institute for Developmental Biology Spemannstrasse 35, 72076 Tübingen, Germany

*To whom correspondence should be addressed. Tel: +49 7071 601 451; Fax: +49 7071 601 349; Email: johannes.soeding{at}tuebingen.mpg.de

Received February 14, 2006. Revised February 21, 2006. Accepted February 21, 2006.

HHsenser is the first server to offer exhaustive intermediate profile searches, which it combines with pairwise comparison of hidden Markov models. Starting from a single protein sequence or a multiple alignment, it can iteratively explore whole superfamilies, producing few or no false positives. The output is a multiple alignment of all detected homologs. HHsenser's sensitivity should make it a useful tool for evolutionary studies. It may also aid applications that rely on diverse multiple sequence alignments as input, such as homology-based structure and function prediction, or the determination of functional residues by conservation scoring and functional subtyping.

HHsenser can be accessed at http://hhsenser.tuebingen.mpg.de/. It has also been integrated into our structure and function prediction server HHpred (http://hhpred.tuebingen.mpg.de/) to improve predictions for near-singleton sequences.


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