GT-Scan

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Abstract

  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).
  
  Author information: 
  (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
  Permissions, please e-mail: journals.permissions@oup.com.
  
  DOI: 10.1093/bioinformatics/btu354 
  PMCID: PMC4155256
  PMID: 24860161  [Indexed for MEDLINE]