CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins
By D. Couvin, A. Bernheim, C. Toffano-Nioche, Marie Touchon, Juraj Michalik, Bertrand Néron, Eduardo P. C. Rocha, Gilles Vergnaud, D. Gautheret, Christine Pourcel. Nucleic Acids Res., 2018
1,362 citations recorded by the source corpus.
Abstract CRISPR (clustered regularly interspaced short palindromic repeats) arrays and their associated (Cas) proteins confer bacteria and archaea adaptive immunity against exogenous mobile genetic elements, such as phages or plasmids. CRISPRCasFinder allows the identification of both CRISPR arrays and Cas proteins. The program includes: (i) an improved CRISPR array detection tool facilitating expert validation based on a rating system, (ii) prediction of CRISPR orientation and (iii) a Cas protein detection and typing tool updated to match the latest classification scheme of these systems. CRISPRCasFinder can either be used online or as a standalone tool compatible with Linux operating system. All third-party software packages employed by the program are freely available. CRISPRCasFinder is available at https://crisprcas.i2bc.paris-saclay.fr.
Subfields: Genetics, Molecular Biology
View Paper: https://www.semanticscholar.org/paper/8c5b8e910b2c332e9e97f4a49111eacf350296bf
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Citations in the corpus
- Critical Assessment of Metagenome Interpretation: the second round of challenges (2021, background): “We evaluated 95 results for 18 binner versions on short-read assemblies: 22 for the strain-madness GSAs, 17 for the strain-madness MEGAHIT assembly (MA), 19 for marine MA, 15 for marine GSA, 12 for plant-associated GSA and ten for the plant-associated MA (Supplementary Tables 9–15).”
- Proksee: in-depth characterization and visualization of bacterial genomes (2023, background): “…for annotating specific bacterial genetic features; for example, the CARD / RGI system for identifying determinants of antimicrobial resistance ( 10 ), IslandViewer for annotating genomic islands ( 11 ), Phigaro for annotating prophage ( 12 ), and CRISPR / Cas Finder for annotating CRISPRs ( 13 ).”