Bioinformatics for CRISPR Biology
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Welcome to a comparison between software for analysing CRISPR-Cas loci in microbial genomes
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The systems consist of a 1) CRISPR ncRNA arrays, 2) Cas proteins, 3) possibly a tracrRNA and 4) target other nucleic caids (e.g. bacteriophage viral genomes)
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Email suggestions to the Author, Chris Brown
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Main functionWeb toolIn Pipeline
Ease of local Install, ease
Speed s/genomeRNA DirectionUser control (score 1-5)Graphic output
Detailed output (score 1-5)
Major AdvantageMajor limitationCommentsInput formatOutput format
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1. Genome analysis (including draft genomes)
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CRISPRDetect (2016)Find CRISPR RNAYesNocli, 15Yes (CRISPRDirection)413
Web based, link to CRISPRTarget (currently not implemented)
Type classification poor
Integrated with other tools
fa, gbk, gbffCD format, tab
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CRISPRFinder (2007)Find CRISPR RNAYesYesNANANo322Well known and citedDoes not predict direction
Integrated with other tools
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CRT (2007)Find CRISPR RNANoNCBI, JGIcli, 5No111Has been incorporated into pipelinesDoes not predict direction
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Piler-CR (2007)Find CRISPR RNANoNCBI, JGIcli, 4No111Has been incorporated into pipelinesDoes not predict direction
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Minced (2014) Find CRISPR RNAYes
Prokka, CRISPRDisco
No111Automatic with CDS annotation in prokkaDoes not predict direction
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CRISPRCompar (2008)Find CRISPR, CasYesNoNo32Only program that compares arrays
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CRISPRone YesNoNANA2
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CRISPRCasFinder (2018)Find CRISPR, CasYesNoDockerYes (CRISPRDirection)4Self target, PAM
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STSS (2018)
Find CRISPR, Cas, Repeat Class, Detect Self match
No
Finds self targets
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CRISPRDisco (2018)Find CRISPR, CasNo
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CRF (2017)Find CRISPR RNA
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Metagenome analysis
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Meta-CRTFind CRISPR in metagenomeNo
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CRISPR type classification
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CRISPRMap (2013)Repeat ClassificationYesNo
Yes (CRISPRStrand)
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Only focussed repeat/type classification tool
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2) Cas proteins
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Usually detected by automated annotation in pipelines - can use hmm (e.g from Makarova et al 2015 or Burstein et al 2015)
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CRISPRDisco, STSS, CasFinder,
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3) TracrRNA
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Chyou et al 2019
Find CRISPR using CRISPRDetect, Cas9 using PSIBLAST and HMMsearch, and then find tracrRNA
YesNoNA
Yes (algorithm run on both strands)
Only general-purpose tracrRNA predictor. CRISPR Array direction not required. Can predict tracrRNAs with no significant similarity between anti-repeat and repeat.
Lack of a good reliability score
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4) Spacer Target analysis
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CRISPRTarget (2013)Find spacer targetYesNoOnly focussed target toolSlow, only onlineScore +1/-1
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blastn -mode shortFind spacer targetYesNoGeneric program, faster
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CRISPR Leader/Promoter analysis
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CRISPRLeader (2016)Promoter alignmentNoNoOnly focussed leader tool
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Other
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CRISPRDirection (2014)Predicts direction of arrayNoIncluded in CRISPRDetect
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CRISPRStrand (2014)Predicts direction of arrayNoIncluded in CRISPRMap
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CRISPRViz (2018)Visualises multiple arrays
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CRISPRStudio (2018)Visualises array
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CRISPRCasViewerVisualises array and Cas genes
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https://github.com/nick-youngblut/CLdb
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dnasko/CASC: CASC Ain't Simply CRT
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GitHub - TrinhLab/CASPERpam: Python code and source files used to identify and analyze PAM sequences for the complete NCBI spacerome
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https://github.com/mitmedialab/SPAMALOT
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CasLocusAnno/bin at master · RiversDong/CasLocusAnno
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