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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 Torres, Néstor V.

PloS one, 2014-10, Vol.9 (10), p.e110726-e110726 [Periódico revisado por pares]

United States: Public Library of Science

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  • Título:
    MacSyFinder: a program to mine genomes for molecular systems with an application to CRISPR-Cas systems
  • Autor: Abby, Sophie S ; Néron, Bertrand ; Ménager, Hervé ; Touchon, Marie ; Rocha, Eduardo P C
  • Torres, Néstor V.
  • Assuntos: Acids ; Analogs ; Bioinformatics ; Biological evolution ; Biology and Life Sciences ; Computer and Information Sciences ; CRISPR ; CRISPR-Cas Systems - genetics ; Data Mining ; Data processing ; Evolution ; Genes ; Genome, Human ; Genomes ; Genomics ; Homology ; Humans ; Identification ; Life Sciences ; Machinery and equipment ; Macromolecules ; Markov chains ; Markov processes ; Molecular modelling ; Prokaryotes ; Proteins ; Quantitative Methods ; Research and Analysis Methods ; Software ; Trends ; Unstructured data
  • É parte de: PloS one, 2014-10, Vol.9 (10), p.e110726-e110726
  • Notas: ObjectType-Article-1
    SourceType-Scholarly Journals-1
    ObjectType-Feature-2
    content type line 23
    PMCID: PMC4201578
    Competing Interests: The authors have declared that no competing interests exist.
    Conceived and designed the experiments: SSA EPCR MT. Performed the experiments: SSA MT. Analyzed the data: MT. Contributed to the writing of the manuscript: SSA EPCR MT. Designed the MacSyFinder software: SSA BN. Designed the MacSyView application: SSA BN HM.
  • Descrição: 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. 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. 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.
  • Editor: United States: Public Library of Science
  • Idioma: Inglês
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