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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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