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

Summary: MOODS (MOtif Occurrence Detection Suite) is a software package for matching position weight matrices against DNA sequences. MOODS implements state-of-the-art online matching algorithms, achieving considerably faster scanning speed than with a simple brute-force search. MOODS is written in C...

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Autores principales: Korhonen, Janne, Martinmäki, Petri, Pizzi, Cinzia, Rastas, Pasi, Ukkonen, Esko
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2009
Materias:
Applications Note
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2778336/
https://www.ncbi.nlm.nih.gov/pubmed/19773334
http://dx.doi.org/10.1093/bioinformatics/btp554
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author Korhonen, Janne
Martinmäki, Petri
Pizzi, Cinzia
Rastas, Pasi
Ukkonen, Esko
author_facet Korhonen, Janne
Martinmäki, Petri
Pizzi, Cinzia
Rastas, Pasi
Ukkonen, Esko
author_sort Korhonen, Janne
collection PubMed
description Summary: MOODS (MOtif Occurrence Detection Suite) is a software package for matching position weight matrices against DNA sequences. MOODS implements state-of-the-art online 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@helsinki.fi
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spelling pubmed-27783362009-11-18 MOODS: fast search for position weight matrix matches in DNA sequences Korhonen, Janne Martinmäki, Petri Pizzi, Cinzia Rastas, Pasi Ukkonen, Esko Bioinformatics Applications Note Summary: MOODS (MOtif Occurrence Detection Suite) is a software package for matching position weight matrices against DNA sequences. MOODS implements state-of-the-art online 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@helsinki.fi Oxford University Press 2009-12-01 2009-09-22 /pmc/articles/PMC2778336/ /pubmed/19773334 http://dx.doi.org/10.1093/bioinformatics/btp554 Text en © The Author(s) 2009. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/2.0/uk/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Applications Note
Korhonen, Janne
Martinmäki, Petri
Pizzi, Cinzia
Rastas, Pasi
Ukkonen, Esko
MOODS: fast search for position weight matrix matches in DNA sequences
title MOODS: fast search for position weight matrix matches in DNA sequences
title_full MOODS: fast search for position weight matrix matches in DNA sequences
title_fullStr MOODS: fast search for position weight matrix matches in DNA sequences
title_full_unstemmed MOODS: fast search for position weight matrix matches in DNA sequences
title_short MOODS: fast search for position weight matrix matches in DNA sequences
title_sort moods: fast search for position weight matrix matches in dna sequences
topic Applications Note
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2778336/
https://www.ncbi.nlm.nih.gov/pubmed/19773334
http://dx.doi.org/10.1093/bioinformatics/btp554
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