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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
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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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