CRISPRCasTyper: Automated Identification, Annotation, and Classification of CRISPR-Cas Loci
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CRISPRCasTyper : Automated Identification, Annotation, and Classification of CRISPR-Cas Loci. / Russel, Jakob; Pinilla-Redondo, Rafael; Mayo-Muñoz, David; Shah, Shiraz A.; Sørensen, Søren J.
In: CRISPR Journal, Vol. 3, No. 6, 2020, p. 462-469.Research output: Contribution to journal › Journal article › peer-review
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TY - JOUR
T1 - CRISPRCasTyper
T2 - Automated Identification, Annotation, and Classification of CRISPR-Cas Loci
AU - Russel, Jakob
AU - Pinilla-Redondo, Rafael
AU - Mayo-Muñoz, David
AU - Shah, Shiraz A.
AU - Sørensen, Søren J.
PY - 2020
Y1 - 2020
N2 - Automated classification of CRISPR-Cas systems has been challenged by their dynamic nature and expanding classification. Here, we developed CRISPRCasTyper, an automated tool with improved capabilities for identifying and typing CRISPR arrays and cas loci based on the latest nomenclature (44 subtypes/variants). As a novel feature, CRISPRCasTyper uses a machine learning approach to subtype CRISPR arrays based on the sequences of the repeats, which allows the typing of orphan and distant arrays. CRISPRCasTyper provides a graphical output, where CRISPRs and cas operons are visualized as gene maps, thus aiding annotation of partial and novel systems through synteny. CRISPRCasTyper was benchmarked against a manually curated set of 31 subtypes with a median accuracy of 98.6% and used to explore CRISPR-Cas diversity across >3,000 metagenomes. Altogether, we present an up-to-date software for improved automated prediction of CRISPR-Cas loci. CRISPRCasTyper is available through conda and as a web server (cctyper.crispr.dk).
AB - Automated classification of CRISPR-Cas systems has been challenged by their dynamic nature and expanding classification. Here, we developed CRISPRCasTyper, an automated tool with improved capabilities for identifying and typing CRISPR arrays and cas loci based on the latest nomenclature (44 subtypes/variants). As a novel feature, CRISPRCasTyper uses a machine learning approach to subtype CRISPR arrays based on the sequences of the repeats, which allows the typing of orphan and distant arrays. CRISPRCasTyper provides a graphical output, where CRISPRs and cas operons are visualized as gene maps, thus aiding annotation of partial and novel systems through synteny. CRISPRCasTyper was benchmarked against a manually curated set of 31 subtypes with a median accuracy of 98.6% and used to explore CRISPR-Cas diversity across >3,000 metagenomes. Altogether, we present an up-to-date software for improved automated prediction of CRISPR-Cas loci. CRISPRCasTyper is available through conda and as a web server (cctyper.crispr.dk).
U2 - 10.1089/crispr.2020.0059
DO - 10.1089/crispr.2020.0059
M3 - Journal article
C2 - 33275853
VL - 3
SP - 462
EP - 469
JO - CRISPR Journal
JF - CRISPR Journal
SN - 2573-1599
IS - 6
ER -
ID: 252770633