Format

Send to

Choose Destination
FEBS Lett. 2019 Sep;593(18):2646-2654. doi: 10.1002/1873-3468.13519. Epub 2019 Jul 17.

CasLocusAnno: a web-based server for annotating cas loci and their corresponding (sub)types.

Dong C1, Zeng Z1, Pu DK1, Wen QF1, Liu S1, Du MZ2, Sun Y3, Gao YZ1, Rao N1,4,5, Huang J1,4,5, Guo FB1,4,5.

Author information

1
School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China.
2
School of Basic Medical Sciences, Southwest Medical University, Luzhou, China.
3
Institutes for Systems Genetics, West China Hospital, Chengdu, China.
4
Centre for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China.
5
Key Laboratory for Neuroinformation of the Ministry of Education, University of Electronic Science and Technology of China, Chengdu, China.

Abstract

In prokaryotes, Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and CRISPR-associated protein (Cas) systems constitute adaptive immune systems against mobile genetic elements (MGEs). Here, we introduce the Markov cluster algorithm (MCL) to Makarova et al.'s method in order to select a more reasonable profile. Additionally, our new Maximum Continuous Cas Subcluster (MCCS) method helps identification of tightly clustered loci. The comparison with two other commonly used programs shows that the method could identify Cas proteins with higher accuracy and lower Additional Prediction Rate (APR). Moreover, we developed a web-based server, CasLocusAnno (http://cefg.uestc.cn/CasLocusAnno), capable of annotating Cas proteins, cas loci and their (sub)types less than ~ 28 s following the whole proteome sequence submission. Its standalone version can be downloaded at https://github.com/RiversDong/CasLocusAnno.

KEYWORDS:

(sub)type annotation; Cas protein annotation; cas locus annotation

PMID:
31260103
DOI:
10.1002/1873-3468.13519

Supplemental Content

Full text links

Icon for Wiley
Loading ...
Support Center