CRISPRcasIdentifier: Machine learning for accurate identification and classification of CRISPR-Cas systems

Abstract: Background
CRISPR-Cas genes are extraordinarily diverse and evolve rapidly when compared to other prokaryotic genes. With the rapid increase in newly sequenced archaeal and bacterial genomes, manual identification of CRISPR-Cas systems is no longer viable. Thus, an automated approach is required for advancing our understanding of the evolution and diversity of these systems and for finding new candidates for genome engineering in eukaryotic models.

Results
We introduce CRISPRcasIdentifier, a new machine learning–based tool that combines regression and classification models for the prediction of potentially missing proteins in instances of CRISPR-Cas systems and the prediction of their respective subtypes. In contrast to other available tools, CRISPRcasIdentifier can both detect cas genes and extract potential association rules that reveal functional modules for CRISPR-Cas systems. In our experimental benchmark on the most recently published and comprehensive CRISPR-Cas system dataset, CRISPRcasIdentifier was compared with recent and state-of-the-art tools. According to the experimental results, CRISPRcasIdentifier presented the best Cas protein identification and subtype classification performance.

Conclusions
Overall, our tool greatly extends the classification of CRISPR cassettes and, for the first time, predicts missing Cas proteins and association rules between Cas proteins. Additionally, we investigated the properties of CRISPR subtypes. The proposed tool relies not only on the knowledge of manual CRISPR annotation but also on models trained using machine learning

Standort
Deutsche Nationalbibliothek Frankfurt am Main
Umfang
Online-Ressource
Sprache
Englisch
Anmerkungen
GigaScience. - 9, 6 (2020) , giaa062, ISSN: 2047-217X

Ereignis
Veröffentlichung
(wo)
Freiburg
(wer)
Universität
(wann)
2020
Urheber
Padilha, Victor A.
Alkhnbashi, Omer S.
Shah, Shiraz A.
Carvalho, André C. P. L. f. de
Backofen, Rolf

DOI
10.1093/gigascience/giaa062
URN
urn:nbn:de:bsz:25-freidok-1663467
Rechteinformation
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Letzte Aktualisierung
14.08.2025, 10:50 MESZ

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Beteiligte

Entstanden

  • 2020

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