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Off-target prediction for CRISPR, need help!


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#1 AllenChiu

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Posted 01 April 2013 - 06:54 PM

We are currently using CRISPR/Cas system(like ZFN or TALEN) for targeted genetic modification in cells of interest, it generally works well, but we want to investigate the specificity of the modification, and thus need to predict and vilidate the possible off-target sites by PCR and subsequent sequencing.
The problem is there is no ideal tools for this purpose, as the only available online software is NCBI Blastn, which always end up with several unintended continuous match using part of our target site as query,whereas we need our whole target site to be query.
So I will be very grateful if you can tell me some Algorithm parameters that will be helpful to keep the whole input sequence (in this case,our whole target site) as query.
Or it also will be very helpful if you know any other online software or local software that can do this job.
Thank you very much!

the attached img is a good example from a recent paper on CRISPR, but the author didn't mention the specific method to achive it.
http://www.nature.co...l/nbt.2507.html

Targeted genome engineering in human cells with the Cas9 RNA-guided endonuclease

Edited by AllenChiu, 01 April 2013 - 06:55 PM.


#2 AllenChiu

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Posted 01 April 2013 - 09:20 PM

up

#3 AllenChiu

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Posted 21 April 2013 - 03:17 AM

up again!

#4 mdfenko

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Posted 22 April 2013 - 04:32 AM

(i admit that i'm not the best person to answer this post but maybe i can start the ball rolling)

have you checked the genomics section of expasy.org?

also, have you looked at the supplement section of the paper you linked for their methodology?

Edited by mdfenko, 22 April 2013 - 04:34 AM.

talent does what it can
genius does what it must
i do what i get paid to do




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