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

Research output: Contribution to journal › Journal article › Research › peer-review

Standard

CRISPRstrand: predicting repeat orientations to determine the crRNA-encoding strand at CRISPR loci. / Alkhnbashi, Omer S.; Costa, Fabrizio; Shah, Shiraz Ali; Garrett, Roger Antony; Saunders, Sita J.; Backofen, Rolf.

In: Bioinformatics, Vol. 30, No. 17, 2014, p. i489-i496.

Research output: Contribution to journal › Journal article › Research › peer-review

Harvard

Alkhnbashi, OS, Costa, F, Shah, SA, Garrett, RA, Saunders, SJ & Backofen, R 2014, 'CRISPRstrand: predicting repeat orientations to determine the crRNA-encoding strand at CRISPR loci', Bioinformatics, vol. 30, no. 17, pp. i489-i496. https://doi.org/10.1093/bioinformatics/btu459

APA

Alkhnbashi, O. S., Costa, F., Shah, S. A., Garrett, R. A., Saunders, S. J., & Backofen, R. (2014). CRISPRstrand: predicting repeat orientations to determine the crRNA-encoding strand at CRISPR loci. Bioinformatics, 30(17), i489-i496. https://doi.org/10.1093/bioinformatics/btu459

Vancouver

Alkhnbashi OS, Costa F, Shah SA, Garrett RA, Saunders SJ, Backofen R. CRISPRstrand: predicting repeat orientations to determine the crRNA-encoding strand at CRISPR loci. Bioinformatics. 2014;30(17):i489-i496. https://doi.org/10.1093/bioinformatics/btu459

Author

Alkhnbashi, Omer S. ; Costa, Fabrizio ; Shah, Shiraz Ali ; Garrett, Roger Antony ; Saunders, Sita J. ; Backofen, Rolf. / CRISPRstrand: predicting repeat orientations to determine the crRNA-encoding strand at CRISPR loci. In: Bioinformatics. 2014 ; Vol. 30, No. 17. pp. i489-i496.

Bibtex

@article{71a3cbba8e144b0b82f1847dd57dc66e,
title = "CRISPRstrand: predicting repeat orientations to determine the crRNA-encoding strand at CRISPR loci",
abstract = "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.",
author = "Alkhnbashi, {Omer S.} and Fabrizio Costa and Shah, {Shiraz Ali} and Garrett, {Roger Antony} and Saunders, {Sita J.} and Rolf Backofen",
year = "2014",
doi = "10.1093/bioinformatics/btu459",
language = "English",
volume = "30",
pages = "i489--i496",
journal = "Computer Applications in the Biosciences",
issn = "1471-2105",
publisher = "Oxford University Press",
number = "17",

}

RIS

TY - JOUR

T1 - CRISPRstrand: predicting repeat orientations to determine the crRNA-encoding strand at CRISPR loci

AU - Alkhnbashi, Omer S.

AU - Costa, Fabrizio

AU - Shah, Shiraz Ali

AU - Garrett, Roger Antony

AU - Saunders, Sita J.

AU - Backofen, Rolf

PY - 2014

Y1 - 2014

N2 - 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.

AB - 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.

U2 - 10.1093/bioinformatics/btu459

DO - 10.1093/bioinformatics/btu459

M3 - Journal article

C2 - 25161238

VL - 30

SP - i489-i496

JO - Computer Applications in the Biosciences

JF - Computer Applications in the Biosciences

SN - 1471-2105

IS - 17

ER -

ID: 124221748