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

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.

Domaines

Fichier principal

10_24072_pcjournal_250.pdf (3.81 Mo)

Licence	Paternité

Cite swh:1:dir:916c9e456eb38ed80f5bab9d5ef64c6b07750c5a;origin=https://github.com/gem-pasteur/macsyfinder;visit=swh:1:snp:be6f94d82f11702214af35de13a426a280c77353;anchor=swh:1:rev:170f481af06ee6bffafdd7de70034ebeeb6da58c Logiciel

Cite 10.6084/m9.figshare.21581280 Jeu de données Abby, S. (2022). Test dataset for MacSyFinder (v2) and expected output files [Data set]. figshare. https://doi.org/10.6084/M9.FIGSHARE.21581280
Two sets of examples with corresponding command lines and expected input and output files are provided on the Figshare platform

Cite 10.6084/m9.figshare.21716426.v1 Jeu de données Abby, S. (2022). A comprehensive test dataset for MacSyFinder v2 with TXSScan [Data set]. figshare. https://doi.org/10.6084/M9.FIGSHARE.21716426.V1

Connectez-vous pour contacter le contributeur

https://pasteur.hal.science/pasteur-04060331

Soumis le : jeudi 6 avril 2023-10:42:21

Dernière modification le : jeudi 6 novembre 2025-18:26:07

Dates et versions

pasteur-04060331 , version 1 (21-10-2022)

pasteur-04060331 , version 2 (06-04-2023)

Licence

Paternité

Identifiants

HAL Id : pasteur-04060331 , version 2
DOI : 10.24072/pcjournal.250

Citer

Bertrand Néron, Rémi Denise, Charles Coluzzi, Marie Touchon, Eduardo P.C. Rocha, et al.. MacSyFinder v2: Improved modelling and search engine to identify molecular systems in genomes. Peer Community Journal, 2023, 3, pp.e28. ⟨10.24072/pcjournal.250⟩. ⟨pasteur-04060331v2⟩