To cite GT-Scan
- GT-Scan: Identifying unique genomic targets
Aidan O'Brien; Timothy L. Bailey
1. Bioinformatics. 2014 Sep 15;30(18):2673-5. doi: 10.1093/bioinformatics/btu354.
Epub 2014 May 23.
GT-Scan: identifying unique genomic targets.
O'Brien A(1), Bailey TL(1).
(1)Genomics and Computational Biology, Institute for Molecular Bioscience, The
University of Queensland, Brisbane, Qld. 4072, Australia.
A number of technologies, including CRISPR/Cas, transcription activator-like
effector nucleases and zinc-finger nucleases, allow the user to target a chosen
locus for genome editing or regulatory interference. Specificity, however, is a
major problem, and the targeted locus must be chosen with care to avoid
inadvertently affecting other loci ('off-targets') in the genome. To address this
we have created 'Genome Target Scan' (GT-Scan), a flexible web-based tool that
ranks all potential targets in a user-selected region of a genome in terms of how
many off-targets they have. GT-Scan gives the user flexibility to define the
desired characteristics of targets and off-targets via a simple 'target rule',
and its interactive output allows detailed inspection of each of the most
promising candidate targets. GT-Scan can be used to identify optimal targets for
CRISPR/Cas systems, but its flexibility gives it potential to be adapted to other
genome-targeting technologies as well.AVAILABILITY AND IMPLEMENTATION: GT-Scan
can be run via the web at: http://gt-scan.braembl.org.au.
© The Author 2014. Published by Oxford University Press. All rights reserved. For
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PMID: 24860161 [Indexed for MEDLINE]