CRISPRdigger: detecting CRISPRs with better direct repeat annotations.
Clustered regularly interspaced short palindromic repeats (CRISPRs) are important genetic elements in many bacterial and archaeal genomes, and play a key role in prokaryote immune systems' fight against invasive foreign elements. The CRISPR system has also been engineered to facilitate target gene editing in eukaryotic genomes. Using the common features of mis-annotated CRISPRs in prokaryotic genomes, this study proposed an accurate de novo CRISPR annotation program CRISPRdigger, which can take a partially assembled genome as its input. A comprehensive comparison with the three existing programs demonstrated that CRISPRdigger can recover more Direct Repeats (DRs) for CRISPRs and achieve a higher accuracy for a query genome. The program was implemented by Perl and all the parameters had default values, so that a user could annotate CRISPRs in a query genome by supplying only a genome sequence in the FASTA format. All the supplementary data are available at http://www.healthinformaticslab.org/supp/.
Shenzhen Institutes of Advanced Technology, and Key Lab for Health Informatics, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, China.|Shenzhen College of Advanced Technology, University of Chinese Academy of Sciences, Shenzhen, Guangdong, 518055, China.
Ruiquan
R
Ge
Shenzhen Institutes of Advanced Technology, and Key Lab for Health Informatics, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, China.|Center for Synthetic Biology Engineering Research, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, China.
Guoqin
G
Mai
Shenzhen Institutes of Advanced Technology, and Key Lab for Health Informatics, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, China.|Shenzhen College of Advanced Technology, University of Chinese Academy of Sciences, Shenzhen, Guangdong, 518055, China.
Pu
P
Wang
Shenzhen Institutes of Advanced Technology, and Key Lab for Health Informatics, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, China.|Shenzhen College of Advanced Technology, University of Chinese Academy of Sciences, Shenzhen, Guangdong, 518055, China.
Manli
M
Zhou
School of Science, Hubei University of Technology, Wuhan, Hubei, 430068, China.
Youxi
Y
Luo
Shenzhen Institutes of Advanced Technology, and Key Lab for Health Informatics, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, China.
Yunpeng
Y
Cai
College of Computer Science and Technology, Changchun, Jilin, 130012, China.|Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin 130012, China.
Fengfeng
F
Zhou
D064113:CRISPR-Cas Systems; D002874:Chromosome Mapping; D003013:Clostridium / Q000235:genetics*; D064112:Clustered Regularly Interspaced Short Palindromic Repeats; D030561:Databases, Nucleic Acid; D020745:Genome, Archaeal; D016680:Genome, Bacterial; D063747:Methanocaldococcus / Q000235:genetics*; D058977:Molecular Sequence Annotation; D012984:Software