MacSyFinder: A Program to Mine Genomes for Molecular Systems with an Application to CRISPR-Cas Systems

Abstract

MotivationBiologists 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 ImplementationMacSyFinder 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.

Genetic and life-history traits associated with the distribution of prophages in bacteria

“…Clusters of cas genes were identified and classified using MacSyFinder (Abby et al , 2014). CRISPR arrays were identified following a previously published methodology (Touchon et al , 2011).…”

Comparative Genomics and Transcriptional Analysis of Flavobacterium columnare Strain ATCC 49512

“…CAS elements were identified using MacSyFinder (Abby et al, 2014). Maximal E -value was set at 1.0, maximal independent E -value was 0.001, and minimal profile coverage parameters were set for CAS element identification.…”

CasLocusAnno: a web‐based server for annotating cas loci and their corresponding (sub)types

“…macsyfinder is an excellent genome mining software program that selects a profile with the highest score when facing a potential Cas protein with multiple profiles. It is therefore challenging for this program to pick the accurate profiles for multidomain proteins, such as the fused Cas protein, in which multiprofiles match the same target sequence.…”

“…The three methods (CasLocusAnno, Makarova et al and MACSYFINDER) identified 8447, 9327 and 7939 Cas proteins in all cas loci, respectively (Fig. 3C) MACSYFINDER is an excellent genome mining software program [27] that selects a profile with the highest score when facing a potential Cas protein with multiple profiles. It is therefore challenging for this program to pick the accurate profiles for multidomain proteins, Our developed web-based server, CasLocusAnno, allows users to submit data via three forms…”