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The HHpred interactive server for protein homology detection and structure prediction
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, 2005. Revised March 21, 2005. Accepted March 21, 2005.
HHpred is a fast server for remote protein homology detection and structure prediction and is the first to implement pairwise comparison of profile hidden Markov models (HMMs). It allows to search a wide choice of databases, such as the PDB, SCOP, Pfam, SMART, COGs and CDD. It accepts a single query sequence or a multiple alignment as input. Within only a few minutes it returns the search results in a user-friendly format similar to that of PSI-BLAST. Search options include local or global alignment and scoring secondary structure similarity. HHpred can produce pairwise query-template alignments, multiple alignments of the query with a set of templates selected from the search results, as well as 3D structural models that are calculated by the MODELLER software from these alignments. A detailed help facility is available. As a demonstration, we analyze the sequence of SpoVT, a transcriptional regulator from Bacillus subtilis. HHpred can be accessed at http://protevo.eb.tuebingen.mpg.de/hhpred.
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