MacSyFinder: A program to mine genomes for molecular systems with an application to CRISPR-Cas systems

PLoS ONE

Volumn 9, Issue 10, 2014, Pages

  Abby, Sophie S ^a,b   Néron, Bertrand ^a   Ménager, Hervé ^a   Touchon, Marie ^a,b   Rocha, Eduardo P C ^a,b  

^a INSTITUT PASTEUR   (France)

^b CNRS   (France)

Author keywords

[No Author keywords available]

Indexed keywords

CELLULAR APOPTOSIS SUSCEPTIBILITY PROTEIN;

ARTICLE; BIOINFORMATICS; CLASSIFICATION ALGORITHM; CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEAT; COMPUTER INTERFACE; CONTROLLED STUDY; DATA ANALYSIS SOFTWARE; DATA MINING; GENOMICS; HIDDEN MARKOV MODEL; MACROMOLECULE; PROCESS DESIGN; PROCESS DEVELOPMENT; PROCESS MODEL; PROCESS MONITORING; PROCESS TECHNOLOGY; SEQUENCE HOMOLOGY; SYSTEM ANALYSIS; VALIDATION PROCESS; COMPUTER PROGRAM; CRISPR CAS SYSTEM; GENETICS; HUMAN; HUMAN GENOME;

CRISPR-CAS SYSTEMS; DATA MINING; GENOME, HUMAN; GENOMICS; HUMANS; SOFTWARE;

EID: 84908136421     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0110726     Document Type: Article

References (28)

1. Alberts B (1998) The cell as a collection of protein machines: preparing the next generation of molecular biologists. Cell 92: 291-294.
2. Pereira-Leal JB, Levy ED, Teichmann SA (2006) The origins and evolution of functional modules: lessons from protein complexes. Philos Trans R Soc Lond B Biol Sci 361: 507-517.
3. Michel B, Grompone G, Florès MJ, Bidnenko V (2004) Multiple pathways process stalled replication forks. Proc Natl Acad Sci U S A 101: 12783-12788.
4. Abby SS, Rocha EP (2012) The non-flagellar type III secretion system evolved from the bacterial flagellum and diversified into host-cell adapted systems. PLoS Genet 8: e1002983.
5. Galagan JE, Nusbaum C, Roy A, Endrizzi MG, Macdonald P, et al. (2002) The genome of M. acetivorans reveals extensive metabolic and physiological diversity. Genome Res 12: 532-542.
6. Huynen M, Snel B, Lathe W 3rd, Bork P (2000) Predicting protein function by genomic context: quantitative evaluation and qualitative inferences. Genome Res 10: 1204-1210.
7. Overbeek R, Fonstein M, D'Souza M, Pusch GD, Maltsev N (1999) The use of gene clusters to infer functional coupling. Proc Natl Acad Sci USA 96: 2896-2901.
8. Lathe WC, Snel B, Bork P (2000) Gene context conservation of a higher order than operons. Trends Biochem Sci 25: 474-479.
9. Zaslaver A, Mayo A, Ronen M, Alon U (2006) Optimal gene partition into operons correlates with gene functional order. Phys Biol 3: 183-189.
10. Finn RD, Tate J, Mistry J, Coggill PC, Sammut SJ, et al. (2008) The Pfam protein families database. Nucleic Acids Res 36: D281-288.
11. Haft DH, Loftus BJ, Richardson DL, Yang F, Eisen JA, et al. (2001) TIGRFAMs: a protein family resource for the functional identification of proteins. Nucleic Acids Res 29: 41-43.
12. Servant F, Bru C, Carrere S, Courcelle E, Gouzy J, et al. (2002) ProDom: automated clustering of homologous domains. Brief Bioinform 3: 246-251.
13. Eddy SR (2011) Accelerated Profile HMM Searches. PLoS Comput Biol 7: e1002195.
14. Barrangou R, Marraffini LA (2014) CRISPR-Cas systems: Prokaryotes upgrade to adaptive immunity. Mol Cell 54: 234-244.
15. Hsu PD, Lander ES, Zhang F (2014) Development and Applications of CRISPR-Cas9 for Genome Engineering. Cell 157: 1262-1278.
16. Barrangou R (2014) RNA events. Cas9 targeting and the CRISPR revolution. Science 344: 707-708.
17. Bland C, Ramsey TL, Sabree F, Lowe M, Brown K, et al. (2007) CRISPR recognition tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats. BMC Bioinformatics 8: 209.
18. Grissa I, Vergnaud G, Pourcel C (2007) CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats. Nucleic Acids Res 35: W52-57.
19. Edgar RC (2007) PILER-CR: fast and accurate identification of CRISPR repeats. BMC Bioinformatics 8: 18.
20. NCBI {BLAST} executables download website (includes makeblastdb). Available: ftp://ftp.ncbi.nih.gov/blast/executables/LATEST/. Accessed 2014 Sep 28.
21. Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, et al. (2009) BLAST+: architecture and applications. BMC Bioinformatics 10: 421.
22. Eddy SR (1998) Profile hidden Markov models. Bioinformatics 14: 755-763.
23. Haft DH, Selengut JD, Richter RA, Harkins D, Basu MK, et al. (2013) TIGRFAMs and Genome Properties in 2013. Nucleic Acids Res 41: D387-395.
24. Haft DH, Selengut J, Mongodin EF, Nelson KE (2005) A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes. PLoS Comput Biol 1: e60.
25. Makarova KS, Haft DH, Barrangou R, Brouns SJ, Charpentier E, et al. (2011) Evolution and classification of the CRISPR-Cas systems. Nat Rev Microbiol 9: 467-477.
26. Staals RHJ, Brouns SJJ (2013) Distribution and Mechanism of the Type I CRISPR-Cas Systems. In: Barrangou R, Oost Jvd, editors. CRISPR-Cas Systems - RNA-mediated Adaptive Immunity in Bacteria and Archaea. Berlin Heidelberg: Springer Berlin Heidelberg.
27. Touchon M, Rocha EP (2010) The small, slow and specialized CRISPR and anti-CRISPR of Escherichia and Salmonella. PLoS ONE 5: e11126.
28. Bondy-Denomy J, Davidson AR (2014) To acquire or resist: the complex biological effects of CRISPR-Cas systems. Trends Microbiol 22: 218-225.