CRISPR-Cas bioinformatics

Omer S. Alkhnbashi; Tobias Meier; Alexander Mitrofanov; Rolf Backofen; Björn Voß

doi:10.1016/j.ymeth.2019.07.013

CRISPR-Cas bioinformatics

Omer S. Alkhnbashi, Tobias Meier, Alexander Mitrofanov, Rolf Backofen, Björn Voß^*

^*Corresponding author for this work

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

49 Scopus citations

Abstract

Clustered regularly interspaced short palindromic repeats (CRISPR) and their associated proteins (Cas) are essential genetic elements in many archaeal and bacterial genomes, playing a key role in a prokaryote adaptive immune system against invasive foreign elements. In recent years, the CRISPR-Cas system has also been engineered to facilitate target gene editing in eukaryotic genomes. Bioinformatics played an essential role in the detection and analysis of CRISPR systems and here we review the bioinformatics-based efforts that pushed the field of CRISPR-Cas research further. We discuss the bioinformatics tools that have been published over the last few years and, finally, present the most popular tools for the design of CRISPR-Cas9 guides.

Original language	English
Pages (from-to)	3-11
Number of pages	9
Journal	Methods
Volume	172
DOIs	https://doi.org/10.1016/j.ymeth.2019.07.013
State	Published - 1 Feb 2020
Externally published	Yes

Bibliographical note

Publisher Copyright:
© 2019 Elsevier Inc.

Keywords

Anti-CRISPR proteins
Bioinformatics
CRISPR array
CRISPR leader
CRISPR-Cas
Cas genes
Direct repeats
PAM
Spacers
crRNAs

ASJC Scopus subject areas

Molecular Biology
General Biochemistry, Genetics and Molecular Biology

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10.1016/j.ymeth.2019.07.013

Cite this

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title = "CRISPR-Cas bioinformatics",

abstract = "Clustered regularly interspaced short palindromic repeats (CRISPR) and their associated proteins (Cas) are essential genetic elements in many archaeal and bacterial genomes, playing a key role in a prokaryote adaptive immune system against invasive foreign elements. In recent years, the CRISPR-Cas system has also been engineered to facilitate target gene editing in eukaryotic genomes. Bioinformatics played an essential role in the detection and analysis of CRISPR systems and here we review the bioinformatics-based efforts that pushed the field of CRISPR-Cas research further. We discuss the bioinformatics tools that have been published over the last few years and, finally, present the most popular tools for the design of CRISPR-Cas9 guides.",

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doi = "10.1016/j.ymeth.2019.07.013",

language = "English",

volume = "172",

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AU - Alkhnbashi, Omer S.

AU - Meier, Tobias

AU - Mitrofanov, Alexander

AU - Backofen, Rolf

AU - Voß, Björn

PY - 2020/2/1

Y1 - 2020/2/1

N2 - Clustered regularly interspaced short palindromic repeats (CRISPR) and their associated proteins (Cas) are essential genetic elements in many archaeal and bacterial genomes, playing a key role in a prokaryote adaptive immune system against invasive foreign elements. In recent years, the CRISPR-Cas system has also been engineered to facilitate target gene editing in eukaryotic genomes. Bioinformatics played an essential role in the detection and analysis of CRISPR systems and here we review the bioinformatics-based efforts that pushed the field of CRISPR-Cas research further. We discuss the bioinformatics tools that have been published over the last few years and, finally, present the most popular tools for the design of CRISPR-Cas9 guides.

AB - Clustered regularly interspaced short palindromic repeats (CRISPR) and their associated proteins (Cas) are essential genetic elements in many archaeal and bacterial genomes, playing a key role in a prokaryote adaptive immune system against invasive foreign elements. In recent years, the CRISPR-Cas system has also been engineered to facilitate target gene editing in eukaryotic genomes. Bioinformatics played an essential role in the detection and analysis of CRISPR systems and here we review the bioinformatics-based efforts that pushed the field of CRISPR-Cas research further. We discuss the bioinformatics tools that have been published over the last few years and, finally, present the most popular tools for the design of CRISPR-Cas9 guides.

KW - Anti-CRISPR proteins

KW - Bioinformatics

KW - CRISPR array

KW - CRISPR leader

KW - CRISPR-Cas

KW - Cas genes

KW - Direct repeats

KW - PAM

KW - Spacers

KW - crRNAs

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DO - 10.1016/j.ymeth.2019.07.013

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SN - 1046-2023

VL - 172

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EP - 11

JO - Methods

JF - Methods

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CRISPR-Cas bioinformatics

Abstract

Bibliographical note

Keywords

ASJC Scopus subject areas

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