CRISPRdigger: detecting CRISPRs with better direct repeat annotations

Ge, Ruiquan; Mai, Guoqin; Wang, Pu; Zhou, Mingyuan; Luo, Youxi; Cai, Yunpeng; Zhou, Fengfeng

doi:10.1038/srep32942

Cited by 23 publications

(19 citation statements)

References 39 publications

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“…Several programs have been developed to identify CRISPR arrays in genomic sequences, the most frequently cited being CRISPRFinder ( 7 ), CRT ( 8 ) and PILER-CR ( 9 ). Additional programs such as CRISPRDetect ( 10 ), CRISPRdigger ( 11 ) and CRF ( 12 ) are also available. Three programs have been proposed for CRISPR array strand prediction based on the characteristics of the CRISPR repeat and the leader: CRISPRDirection using CRISPRDetect ( 10 , 13 ), CRISPRstrand ( 14 , 15 ) and CRISPRleader ( 16 ).…”

Section: Introductionmentioning

confidence: 99%

CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins

Couvin

Bernheim

Toffano‐Nioche

et al. 2018

Nucleic Acids Research

1,091

828

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CRISPR (clustered regularly interspaced short palindromic repeats) arrays and their associated (Cas) proteins confer bacteria and archaea adaptive immunity against exogenous mobile genetic elements, such as phages or plasmids. CRISPRCasFinder allows the identification of both CRISPR arrays and Cas proteins. The program includes: (i) an improved CRISPR array detection tool facilitating expert validation based on a rating system, (ii) prediction of CRISPR orientation and (iii) a Cas protein detection and typing tool updated to match the latest classification scheme of these systems. CRISPRCasFinder can either be used online or as a standalone tool compatible with Linux operating system. All third-party software packages employed by the program are freely available. CRISPRCasFinder is available at https://crisprcas.i2bc.paris-saclay.fr.

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Section: Introductionmentioning

confidence: 99%

CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins

Couvin

Bernheim

Toffano‐Nioche

et al. 2018

Nucleic Acids Research

1,091

828

View full text Add to dashboard Cite

show abstract

“…CRISPR finder Program Online allowed us to acquire the numbers and sequences of repeats and spacers of CRISPRs [27]. The typical repeats of CRISPR were analyzed through multiple sequence alignment using Cluster X software, and the alignments of these repeats were visualized with WebLogo (http://weblogo.berkeley.edu/logo.cgi).…”

Section: Analysis Methodsmentioning

confidence: 99%

Bioinformatic analysis of Listeria monocytogenes CRISPR

Qu¹,

Shen²,

Xu³

et al. 2018

Oncotarget

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Listeria monocytogenes is a leading causes of death from food-borne pathogens. Bioinformatics approach was applied to investigate the features of L. monocytogenes CRISPR structure and the relationship between CRISPR and plasmid transposase content. Among 93 L. monocytogenes genomes, 95 confirmed CRISPR structure loci were identified and classified into 5 groups based on repeat size. RNA secondary structure and minimum free energy indicated that the secondary structure of Group 5 (36 bp) was more stable than other groups. Type I-B or II-A Cas genes were found in 36 strains, and the CRISPR-Cas system of type I-B was more conserved than type II-A. Furthermore, CRISPR loci affected the enzyme transposase content of L. monocytogenes plasmid. This study examined the diversity of the CRISPR-Cas system in L. monocytogenes, classified CRISPR structure and repeats, and demonstrated the influence of the CRISPR-Cas system on the number of transposase in plasmid.

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“…Carbohydrate-active enzymes were predicted using the carbohydrate-active enzymes database [40]. CRISPRs were identified using CRISPRdigger (version 1.0, https://github.com/ greyspring/CRISPRdigger) [41].…”

Section: Genome Component Prediction and Gene Annotationmentioning

confidence: 99%

Complete Genome Sequence Reveals Evolutionary and Comparative Genomic Features of Xanthomonas albilineans Causing Sugarcane Leaf Scald

et al. 2020

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Leaf scald (caused by Xanthomonas albilineans) is an important bacterial disease affecting sugarcane in most sugarcane growing countries, including China. High genetic diversity exists among strains of X. albilineans from diverse geographic regions. To highlight the genomic features associated with X. albilineans from China, we sequenced the complete genome of a representative strain (Xa-FJ1) of this pathogen using the PacBio and Illumina platforms. The complete genome of strain Xa-FJ1 consists of a circular chromosome of 3,724,581 bp and a plasmid of 31,536 bp. Average nucleotide identity analysis revealed that Xa-FJ1 was closest to five strains from the French West Indies and the USA, particularly to the strain GPE PC73 from Guadeloupe. Comparative genomic analysis between Xa-FJ1 and GPE PC73 revealed prophage integration, homologous recombination, transposable elements, and a clustered regulatory interspaced short palindromic repeats (CRISPR) system that were linked with 16 insertions/deletions (InDels). Ten and 82 specific genes were found in Xa-FJ1 and GPE PC73, respectively, and some of these genes were subjected to phage-related proteins, zona occludens toxin, and DNA methyltransferases. Our findings highlight intra-species genetic variability of the leaf scald pathogen and provide additional genomic resources to investigate its fitness and virulence.

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CRISPRdigger: detecting CRISPRs with better direct repeat annotations

Cited by 23 publications

References 39 publications

CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins

CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins

Bioinformatic analysis of Listeria monocytogenes CRISPR

Complete Genome Sequence Reveals Evolutionary and Comparative Genomic Features of Xanthomonas albilineans Causing Sugarcane Leaf Scald

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