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© ALPS team
Publication : Peer Community Journal

MacSyFinder v2: Improved modelling and search engine to identify molecular systems in genomes

Team: Expertise group : ALPS – Algorithmics and programming in science
Team: Bioinformatics and Biostatistics HUB
Member: Bertrand Néron
Scientific Fields
Diseases
Organisms
Applications
Technique

Published in Peer Community Journal - 24 Mar 2023

Bertrand Néron, Rémi Denise, Charles Coluzzi, Marie Touchon, Eduardo P.C. Rocha, Sophie Abby

Link to HAL – pasteur-04060331

Link to DOI – 10.24072/pcjournal.250

Peer Community Journal, 2023, 3, pp.e28. ⟨10.24072/pcjournal.250⟩

MacSyFinder is a program to model and detect macromolecular systems, genetic pathways… in protein datasets. In prokaryotes, these systems have often evolutionarily conserved properties: they are made of conserved components, they are encoded in compact loci (conserved genetic architecture). The user models these systems with MacSyFinder to reflect these conserved features, and to allow their efficient detection. Criteria for systems detection include component content (quorum), and genomic co-localization. Each component corresponds to a hidden Markov model (HMM) protein profile to perform sequence similarity searches with the program Hmmer.