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MacSyFinder: A Program to Mine Genomes for Molecular Systems with an Application to CRISPR-Cas Systems
MOTIVATION: Biologists often wish to use their knowledge on a few experimental models of a given molecular system to identify homologs in genomic data. We developed a generic tool for this purpose. RESULTS: Macromolecular System Finder (MacSyFinder) provides a flexible framework to model the propert...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2014
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4201578/ https://www.ncbi.nlm.nih.gov/pubmed/25330359 http://dx.doi.org/10.1371/journal.pone.0110726 |
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author | Abby, Sophie S. Néron, Bertrand Ménager, Hervé Touchon, Marie Rocha, Eduardo P. C. |
author_facet | Abby, Sophie S. Néron, Bertrand Ménager, Hervé Touchon, Marie Rocha, Eduardo P. C. |
author_sort | Abby, Sophie S. |
collection | PubMed |
description | MOTIVATION: Biologists often wish to use their knowledge on a few experimental models of a given molecular system to identify homologs in genomic data. We developed a generic tool for this purpose. RESULTS: Macromolecular System Finder (MacSyFinder) provides a flexible framework to model the properties of molecular systems (cellular machinery or pathway) including their components, evolutionary associations with other systems and genetic architecture. Modelled features also include functional analogs, and the multiple uses of a same component by different systems. Models are used to search for molecular systems in complete genomes or in unstructured data like metagenomes. The components of the systems are searched by sequence similarity using Hidden Markov model (HMM) protein profiles. The assignment of hits to a given system is decided based on compliance with the content and organization of the system model. A graphical interface, MacSyView, facilitates the analysis of the results by showing overviews of component content and genomic context. To exemplify the use of MacSyFinder we built models to detect and class CRISPR-Cas systems following a previously established classification. We show that MacSyFinder allows to easily define an accurate “Cas-finder” using publicly available protein profiles. AVAILABILITY AND IMPLEMENTATION: MacSyFinder is a standalone application implemented in Python. It requires Python 2.7, Hmmer and makeblastdb (version 2.2.28 or higher). It is freely available with its source code under a GPLv3 license at https://github.com/gem-pasteur/macsyfinder. It is compatible with all platforms supporting Python and Hmmer/makeblastdb. The “Cas-finder” (models and HMM profiles) is distributed as a compressed tarball archive as Supporting Information. |
format | Online Article Text |
id | pubmed-4201578 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2014 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-42015782014-10-21 MacSyFinder: A Program to Mine Genomes for Molecular Systems with an Application to CRISPR-Cas Systems Abby, Sophie S. Néron, Bertrand Ménager, Hervé Touchon, Marie Rocha, Eduardo P. C. PLoS One Research Article MOTIVATION: Biologists often wish to use their knowledge on a few experimental models of a given molecular system to identify homologs in genomic data. We developed a generic tool for this purpose. RESULTS: Macromolecular System Finder (MacSyFinder) provides a flexible framework to model the properties of molecular systems (cellular machinery or pathway) including their components, evolutionary associations with other systems and genetic architecture. Modelled features also include functional analogs, and the multiple uses of a same component by different systems. Models are used to search for molecular systems in complete genomes or in unstructured data like metagenomes. The components of the systems are searched by sequence similarity using Hidden Markov model (HMM) protein profiles. The assignment of hits to a given system is decided based on compliance with the content and organization of the system model. A graphical interface, MacSyView, facilitates the analysis of the results by showing overviews of component content and genomic context. To exemplify the use of MacSyFinder we built models to detect and class CRISPR-Cas systems following a previously established classification. We show that MacSyFinder allows to easily define an accurate “Cas-finder” using publicly available protein profiles. AVAILABILITY AND IMPLEMENTATION: MacSyFinder is a standalone application implemented in Python. It requires Python 2.7, Hmmer and makeblastdb (version 2.2.28 or higher). It is freely available with its source code under a GPLv3 license at https://github.com/gem-pasteur/macsyfinder. It is compatible with all platforms supporting Python and Hmmer/makeblastdb. The “Cas-finder” (models and HMM profiles) is distributed as a compressed tarball archive as Supporting Information. Public Library of Science 2014-10-17 /pmc/articles/PMC4201578/ /pubmed/25330359 http://dx.doi.org/10.1371/journal.pone.0110726 Text en © 2014 Abby et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited. |
spellingShingle | Research Article Abby, Sophie S. Néron, Bertrand Ménager, Hervé Touchon, Marie Rocha, Eduardo P. C. MacSyFinder: A Program to Mine Genomes for Molecular Systems with an Application to CRISPR-Cas Systems |
title | MacSyFinder: A Program to Mine Genomes for Molecular Systems with an Application to CRISPR-Cas Systems |
title_full | MacSyFinder: A Program to Mine Genomes for Molecular Systems with an Application to CRISPR-Cas Systems |
title_fullStr | MacSyFinder: A Program to Mine Genomes for Molecular Systems with an Application to CRISPR-Cas Systems |
title_full_unstemmed | MacSyFinder: A Program to Mine Genomes for Molecular Systems with an Application to CRISPR-Cas Systems |
title_short | MacSyFinder: A Program to Mine Genomes for Molecular Systems with an Application to CRISPR-Cas Systems |
title_sort | macsyfinder: a program to mine genomes for molecular systems with an application to crispr-cas systems |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4201578/ https://www.ncbi.nlm.nih.gov/pubmed/25330359 http://dx.doi.org/10.1371/journal.pone.0110726 |
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