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CRISPRstrand: predicting repeat orientations to determine the crRNA-encoding strand at CRISPR loci

Publikation: Forskning - peer reviewTidsskriftartikel

Omer S. Alkhnbashi, Fabrizio Costa, Shiraz Ali Shah, Roger Antony Garrett, Sita J. Saunders, Rolf Backofen

Motivation: The discovery of CRISPR-Cas systems almost 20 years ago rapidly changed our perception of the bacterial and archaeal immune systems. CRISPR loci consist of several repetitive DNA sequences called repeats, inter-spaced by stretches of variable length sequences called spacers. This CRISPR array is transcribed and processed into multiple mature RNA species (crRNAs). A single crRNA is integrated into an interference complex, together with CRISPR-associated (Cas) proteins, to bind and degrade invading nucleic acids. Although existing bioinformatics tools can recognize CRISPR loci by their characteristic repeat-spacer architecture, they generally output CRISPR arrays of ambiguous orientation and thus do not determine the strand from which crRNAs are processed. Knowledge of the correct orientation is crucial for many tasks, including the classification of CRISPR conservation, the detection of leader regions, the identification of target sites (protospacers) on invading genetic elements and the characterization of protospacer-adjacent motifs.
OriginalsprogEngelsk
TidsskriftBioinformatics
Vol/bind30
Tidsskriftsnummer17
Sider (fra-til)i489-i496
Antal sider8
ISSN1367-4803
DOI
StatusUdgivet - 2014

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