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MacSyFinder specifications

Information


Unique identifier OMICS_20116
Name MacSyFinder
Alternative name Macromolecular System Finder
Interface Application programming interface
Restrictions to use None
Programming languages Python
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline Sophie Abby

Information


Unique identifier OMICS_20116
Name MacSyFinder
Alternative name Macromolecular System Finder
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data A list of systems defined, protein profiles, command-line parameters and a file with protein sequences.
Input format XML, FASTA
Operating system Unix/Linux, Mac OS, Windows
Programming languages Python
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.0.2
Stability Stable
Requirements
Hmmer, makeblastdb
Maintained Yes

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Documentation


Maintainer


  • person_outline Sophie Abby

Publication for Macromolecular System Finder

MacSyFinder citations

 (14)
library_books

The Genome Sequence of “Candidatus Fokinia solitaria”: Insights on Reductive Evolution in Rickettsiales

2018
Genome Biol Evol
PMCID: 5905368
PMID: 29659807
DOI: 10.1093/gbe/evy072

[…] d using the BioCyc and Pathway Tools suites (; ). Presence of insertion sequences, prophages, secretion systems, and secreted proteins was predicted using, respectively, ISsaga (), PHAST (), TXSScan (MacSyFinder-based; ), SignalP (), and TMHMM () (with default parameters) and comparing the obtained results with the manually curated annotation. […]

library_books

Genome Wide Analysis of Type VI System Clusters and Effectors in Burkholderia Species

2018
PMCID: 5796746
PMID: 29422784
DOI: 10.5423/PPJ.FT.11.2017.0231

[…] red as potential T6SS clusters. The component genes of all clusters were then manually checked in detail. Furthermore, we compared the T6SS clusters obtained here with those detected by using TXSScan MacSyFinder program (; ), to carry out the optimized validation for potential functional systems. In final, the clusters that either were detected by both programs or contained at least 10 core compon […]

library_books

Candidatus Nitrosocaldus cavascurensis, an Ammonia Oxidizing, Extremely Thermophilic Archaeon with a Highly Mobile Genome

2018
Front Microbiol
PMCID: 5797428
PMID: 29434576
DOI: 10.3389/fmicb.2018.00028

[…] ype IV pili), we built HMM profiles (as above except alignments were manually curated for AMO and Ure), based on the corresponding arCOG families and integrated the respective sets of profiles in the MacSyFinder framework that enables the detection of sets of co-localized genes in the genome (parameters inter_gene_max_space = 10, min_nb_mandatory_genes = 1 for AMO and Ure, inter_gene_max_space = 1 […]

library_books

Inhibition of NHEJ repair by type II A CRISPR Cas systems in bacteria

2017
Nat Commun
PMCID: 5727150
PMID: 29234047
DOI: 10.1038/s41467-017-02350-1

[…] NHEJ and type II CRISPR-Cas systems were detected using MacSyFinder (default parameters). The published models were used for the detection of type II CRISPR-Cas systems. To detect NHEJ, we retrieved protein profiles from TIGRFAM: Ku (PF02735) and ligD (TIG […]

library_books

The chromosomal organization of horizontal gene transfer in bacteria

2017
Nat Commun
PMCID: 5635113
PMID: 29018197
DOI: 10.1038/s41467-017-00808-w

[…] ere removed. Integrons were identified using IntegronFinder v.1.4 with the –local_max option. Integrative conjugative elements (ICEs) and integrative mobilizable elements (IMEs) were identified using MacSyFinder v.1.0.2 with TXSScan profiles. Elements with a full conjugative apparatus were classed as ICE, the others as IME (see ref. for criteria). Integrases were identified using the PFAM profile […]

library_books

Comparative Analysis of the Flavobacterium columnare Genomovar I and II Genomes

2017
Front Microbiol
PMCID: 5524665
PMID: 28790987
DOI: 10.3389/fmicb.2017.01375

[…] sed to compute Kimura distance matrix, which was used as input for the Neighbor-Joining algorithm as implemented in the PHYLIP package ().To predict bacterial protein secretion systems, analysis with MacSyFinder was performed using default features (unordered replicon, circular, all available systems, maximal E-value 1.0, maximal independent E-value 0.001, minimal profile coverage 0.5) (). CRISPRF […]


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MacSyFinder institution(s)
Microbial Evolutionary Genomics, Institut Pasteur, Paris, France; UMR3525, CNRS, Paris, France; Centre d’Informatique pour la Biologie, Institut Pasteur, Paris, France
MacSyFinder funding source(s)
Supported by the Institut Pasteur, the French ‘‘Centre National de la Recherche Scientifique’’ and the European Research Council (grant EVOMOBILOME, number 281605).

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