Genome editing strategies are certainly a hot topic of late. We were astonished at the traffic that the animation of the CRISPR/Cas-9 process recently drew to the blog. There’s a huge amount of potential for novel types of studies and interventions in human disease situations–but I’m already seeing applications in agriculture coming along. There’s an edited canola available in Canada already. China has edited wheat for disease resistance. There’s a project underway to remove horns from cattle–by merely snipping out a bit of sequence with TALENs/ZNF strategies. They’ve already created cattle with edited myostatin too.
To accompany this work, new software tools have been developed to help design target sequences and evaluate potential off-target situations. Both TALEN target software tools exist, and CRISPR tools exist. For this post I’ll be focusing on just one of the CRISPR tools, but I’ll list a few others as well. Some sites have incorporated both options in their software tools. Some will have a small range of species, some have larger sets. So part of choosing a tool is asking about the genomes it supports. In future Tips we may explore some of the others. There is something of a flood of these tools coming along, and I’ll continue to explore them.
This week’s focus is CRISPRdirect. A Japanese group has created this tool for generating a guide sequence and for evaluating potential off-target activity. This introductory video (with music, and with English annotations to convey the features) will give you an overview of the functions.
It seems to be an easy-to-use interface, with effective organization of the results. They have a nice range of species to examine–not only some of the mammalian genomes, but fish, chicken, worm, plants, and yeast too. There’s a graphical viewing component and an easy export option as well.
So I’ve come across a few tools in my search, but if you have favorites please feel free to add them below in the comments. I’m going to continue to look into these tools and will be looking to highlight others in the future.
A few links to other tools I’ve been looking at:
TAL Effector Nucleotide Targeter 2.0: https://tale-nt.cac.cornell.edu/
ZiFiT Targeter software (TALEN/ZNF/CRISPR support): http://zifit.partners.org/ZiFiT/
CRISPY (specific for CHO cells): http://staff.biosustain.dtu.dk/laeb/crispy/
Naito Y., K. Hino, H. Bono & K. Ui-Tei (2014). CRISPRdirect: software for designing CRISPR/Cas guide RNA with reduced off-target sites, Bioinformatics, DOI: http://dx.doi.org/10.1093/bioinformatics/btu743