MacSyFinder: a program to mine genomes for molecular systems with an application to CRISPR-Cas systems

PloS One
Sophie S AbbyEduardo P C Rocha

Abstract

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...Continue Reading

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Citations

Mar 17, 2016·Scientific Reports·Sophie S AbbyEduardo P C Rocha
Oct 26, 2016·The ISME Journal·Marie TouchonEduardo Pc Rocha
Nov 27, 2014·Frontiers in Microbiology·Sophie S AbbyGwenael Piganeau
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Oct 27, 2017·International Journal of Systematic and Evolutionary Microbiology·Merete Wiken DeesMay Bente Brurberg
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Sep 25, 2017·Applied and Environmental Microbiology·Nan LiMark J McBride
Mar 25, 2019·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Aude BernheimEduardo P C Rocha
Mar 25, 2019·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Anne ChevallereauClare Rollie
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Aug 10, 2017·Frontiers in Microbiology·Salih KumruAttila Karsi
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Sep 16, 2017·Nucleic Acids Research·Jean CuryEduardo P C Rocha

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Methods Mentioned

BETA
protein profiles

Software Mentioned

Firefox
Hmmer
MacSyView
Chrome
Safari
romolecular Sy stem Finder (
makeblastdb
formatdb
Chromium
Cas

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