Huang, Le, Yang, Bowen, Yi, Haidong, Asif, Amina, Wang, Jiawei, Lithgow, Trevor, Zhang, Han, Minhas, Fayyaz ul Amir Afsar and Yin, Yanbin (2021) AcrDB : a database of anti-CRISPR operons in prokaryotes and viruses. Nucleic Acids Research, 49 (D1). D622-D629. doi:10.1093/nar/gkaa857 ISSN 0305-1048.

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Abstract

CRISPR–Cas is an anti-viral mechanism of prokaryotes that has been widely adopted for genome editing. To make CRISPR–Cas genome editing more controllable and safer to use, anti-CRISPR proteins have been recently exploited to prevent excessive/prolonged Cas nuclease cleavage. Anti-CRISPR (Acr) proteins are encoded by (pro)phages/(pro)viruses, and have the ability to inhibit their host's CRISPR–Cas systems. We have built an online database AcrDB (http://bcb.unl.edu/AcrDB) by scanning ∼19 000 genomes of prokaryotes and viruses with AcrFinder, a recently developed Acr-Aca (Acr-associated regulator) operon prediction program. Proteins in Acr-Aca operons were further processed by two machine learning-based programs (AcRanker and PaCRISPR) to obtain numerical scores/ranks. Compared to other anti-CRISPR databases, AcrDB has the following unique features: (i) It is a genome-scale database with the largest collection of data (39 799 Acr-Aca operons containing Aca or Acr homologs); (ii) It offers a user-friendly web interface with various functions for browsing, graphically viewing, searching, and batch downloading Acr-Aca operons; (iii) It focuses on the genomic context of Acr and Aca candidates instead of individual Acr protein family and (iv) It collects data with three independent programs each having a unique data mining algorithm for cross validation. AcrDB will be a valuable resource to the anti-CRISPR research community.

Item Type:	Journal Article
Subjects:	Q Science > QR Microbiology
Divisions:	Faculty of Science, Engineering and Medicine > Science > Computer Science
Library of Congress Subject Headings (LCSH):	Prokaryotes, Bacteriophages -- Genetics
Journal or Publication Title:	Nucleic Acids Research
Publisher:	Oxford University Press
ISSN:	0305-1048
Official Date:	8 January 2021
Dates:	Date Event 8 January 2021 Published 17 October 2020 Available 17 October 2020 Accepted
Volume:	49
Number:	D1
Page Range:	D622-D629
DOI:	10.1093/nar/gkaa857
Status:	Peer Reviewed
Publication Status:	Published
Access rights to Published version:	Open Access (Creative Commons)
Date of first compliant deposit:	7 January 2021
Date of first compliant Open Access:	8 January 2021
RIOXX Funder/Project Grant:	Project/Grant ID RIOXX Funder Name Funder ID DBI-1933521 National Science Foundation http://dx.doi.org/10.13039/501100008982 58-8042-9-089 U.S. Department of Agriculture http://dx.doi.org/10.13039/100000199 2019-YIN University of Nebraska–Lincoln http://viaf.org/viaf/312587805

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