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Old 01-20-2012, 01:32 PM
Laszlo Kajan
Default Bug#656626: ITP: hhsuite -- sensitive protein sequence searching based on HMM-HMM alignment

Package: wnpp
Severity: wishlist
Owner: Laszlo Kajan <lkajan@rostlab.org>

* Package name : hhsuite
Version : 2.0.4
Upstream Author : Johannes Soeding, Michael Remmert, Andreas Hauser <hauser@genzentrum.lmu.de>, Andreas Biegert
* URL : http://toolkit.genzentrum.lmu.de/sections/search
* License : GPLv3
Programming Lang: C++
Description : sensitive protein sequence searching based on HMM-HMM alignment

The HH-suite is an open-source software package for sensitive protein sequence searching based on the
pairwise alignment of hidden Markov models (HMMs). It contains HHsearch and HHblits
among other programs and utilities.
HHsearch takes as input a multiple sequence alignment (MSA)
or profile HMM and searches a database of HMMs (e.g. PDB, Pfam, or InterPro) for homologous
proteins. HHsearch is often used for protein structure prediction to detect homologous templates
and to build highly accurate query-template pairwise alignments for homology modeling.
HHblits can build high-quality MSAs starting from single sequences or from MSAs. It transforms these into a query HMM
and, using an iterative search strategy, adds significantly similar sequences from the previous search
to the updated query HMM for the next search iteration. Compared to PSI-BLAST, HHblits is
faster, up to twice as sensitive and produces more accurate alignments.

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