What is the best way to find promoter regions in my GOI? I've looked on UCSC genome browser to no avail. The ultimate purpose is to evaluate sgRNA sequences for CRISPRa. Thanks.
Submit your paper to J Biol Methods today!
2 replies to this topic
#2
El Crazy Xabi
-
- Active Members
-
- 245 posts
Veteran
29
Excellent
Excellent
Posted 21 September 2016 - 03:39 PM
Why don't you use a CRISPR target finder then?
Check this one (I haven't used it though):
https://bitbucket.or...ctop_standalone
PS: if your genome is from a commonly used species you can try these ones
(online version of the previous)
http://crispr.cos.un...de/species.html
CRISPR target finder
http://tools.flycris...u/targetFinder/
Edited by El Crazy Xabi, 21 September 2016 - 03:41 PM.
#3
Ken S
-
- Members
-
- 1 posts
member
0
Neutral
Neutral
Posted 22 September 2016 - 01:37 PM
Which CRISPRa system are you using? Look at the publication for it, they probably describe the optimal sgRNA design parameters. Generally, targeting a pool of sgRNAs as close to the transcriptional start site as possible (<100bp) is the best.
