[Biopython] MOODS: fast search for position weight matrix matches in DNA sequences.

[Peter]

Hi all,

I'm forwarding an interesting post from Dave to the BioPerl mailing list, which
should also be of interest here...

Peter

---------- Forwarded message ----------
From: Dave Messina <David.Messina at sbc.su.se>
Date: Thu, Sep 24, 2009 at 10:38 AM
Subject: Re: [Bioperl-l] a Main Page proposal
To: Chris Fields <cjfields at illinois.edu>
Cc: bioperl-l at lists.open-bio.org, Dave Clements
<clements at nescent.org>, Peter <biopython at maubp.freeserve.co.uk>, "Mark
A. Jensen" <maj at fortinbras.us>


>
> Not to add yet more to the list, but I also think a concise list of
> projects using (or 'powered by') bioperl should be front-and-center; not a
> lot of users know when/where bioperl is used.  This applies to the other
> bio* as well, particularly biopython (seeing it popping up more and more).
>


Along these lines, it'd be great to publicize not only
BioPerl-*powered*projects, but ones which interface with it, too.

Just this week, for example, there is this, which could go both on a static
page and in the newsfeed:
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btp554v1

MOODS: fast search for position weight matrix matches in DNA sequences.

Korhonen J, Martinmäki P, Pizzi C, Rastas P, Ukkonen E.
Department of Computer Science and Helsinki Institute for Information
Technology,
University of Helsinki, Helsinki, Finland.

SUMMARY: MOODS (MOtif Occurrence Detection Suite) is a software package for
matching position weight matrices against DNA sequences. MOODS implements
state-of-the-art on-line matching algorithms, achieving considerably faster
scanning speed than with a simple brute-force search. MOODS is written in C++,
with bindings for the popular BioPerl and Biopython toolkits. It can easily be
adapted for different purposes and integrated into existing workflows. It can
also be used as a C++ library. AVAILABILITY: The package with documentation and
examples of usage is available at http://www.cs.helsinki.fi/group/pssmfind. The
source code is also available under the terms of a GNU General Public License
(GPL). CONTACT: janne.h.korhonen at helsinki.fi.

PMID: 19773334 [PubMed - as supplied by publisher]

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