Welcome to MacSyFinder’s documentation!


A new version of MacSyFinder (v2) is available, see here for an overview of the novelties. The search engine was improved, and some bugs/unwanted behaviors corrected. MacSyFinder’s models for v2 are very similar, yet not compatible with those from v1. See here for details on how to carry your models to v2.

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, and 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.

In order to model macromolecular systems, the user:

  • builds or gather from databanks HMM protein profiles for components of interest,
  • defines decision rules for each system in a dedicated XML grammar (see Macromolecular models).


If you use MacSyFinder, please cite:

Abby SS, Néron B, Ménager H, Touchon M, Rocha EPC (2014). MacSyFinder: A Program to Mine Genomes for Molecular Systems with an Application to CRISPR-Cas Systems. PLoS ONE 9(10): e110726. doi:10.1371/journal.pone.0110726

Indices and tables