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2016 ; 17
(ä): 356
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CRISPRDetect: A flexible algorithm to define CRISPR arrays
#MMPMID27184979
Biswas A
; Staals RH
; Morales SE
; Fineran PC
; Brown CM
BMC Genomics
2016[May]; 17
(ä): 356
PMID27184979
show ga
BACKGROUND: CRISPR (clustered regularly interspaced short palindromic repeats)
RNAs provide the specificity for noncoding RNA-guided adaptive immune defence
systems in prokaryotes. CRISPR arrays consist of repeat sequences separated by
specific spacer sequences. CRISPR arrays have previously been identified in a
large proportion of prokaryotic genomes. However, currently available detection
algorithms do not utilise recently discovered features regarding CRISPR loci.
RESULTS: We have developed a new approach to automatically detect, predict and
interactively refine CRISPR arrays. It is available as a web program and command
line from bioanalysis.otago.ac.nz/CRISPRDetect. CRISPRDetect discovers putative
arrays, extends the array by detecting additional variant repeats, corrects the
direction of arrays, refines the repeat/spacer boundaries, and annotates
different types of sequence variations (e.g. insertion/deletion) in near
identical repeats. Due to these features, CRISPRDetect has significant advantages
when compared to existing identification tools. As well as further support for
small medium and large repeats, CRISPRDetect identified a class of arrays with
'extra-large' repeats in bacteria (repeats 44-50 nt). The CRISPRDetect output is
integrated with other analysis tools. Notably, the predicted spacers can be
directly utilised by CRISPRTarget to predict targets. CONCLUSION: CRISPRDetect
enables more accurate detection of arrays and spacers and its gff output is
suitable for inclusion in genome annotation pipelines and visualisation. It has
been used to analyse all complete bacterial and archaeal reference genomes.
|*CRISPR-Cas Systems
[MESH]
|*Clustered Regularly Interspaced Short Palindromic Repeats
[MESH]
free
free
free
