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Question: CFDscore calculations used in CRISPRseek
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gravatar for Dawid G. Nowak
6 weeks ago by
United States
Dawid G. Nowak10 wrote:

Hi,

I have a question about “CFDscore" calculations used in CRISPRseek. I have a guide that I am testing against target DNA sequence using compare2Sequences(). I see some differences when I compare a table manually to the calculated score using compare2Sequences(). Just to be sure how “CFDscore" is implemented and before I go to details with my sequence, I would appreciate answers to the below questions

Questions:
1) Is “CFDscore” in CRISPRseek is calculated based on the table “NatureBiot2016SuppTable19DoenchRoot" (Doench et al., 2016) and Percent-Active column? 

2) I have a guide:DNA mismatch (only one mismatch) in position 1, rA:dG, Percent-Active columns gives a score: 0.857. Does it mean this number is used as a score or there is another parameter using this score and recalculating the final CFDscore?

2) If there is a guide:DNA mismatch that doesn’t exist in the table i.e. rU:dA how the score is calculated?

Thanks,
Dawid

ADD COMMENTlink modified 6 weeks ago by Julie Zhu3.8k • written 6 weeks ago by Dawid G. Nowak10
1
gravatar for Julie Zhu
6 weeks ago by
Julie Zhu3.8k
United States
Julie Zhu3.8k wrote:
Dawid, 1. Yes, “CFDscore” in CRISPRseek is calculated based on the table “NatureBiot2016SuppTable19DoenchRoot" (Doench et al., 2016) and Percent-Active column. 2. CFDscore is calculated using mismatch type and mismatch position although the mismatch activity is given as pos 20, 19, 18,....1 distance from PAM. In addition, PAM sequence affects the CFDscore specified as subPAM.activity = hash( AA =0, AC = 0, AG = 0.259259259, AT = 0, CA = 0, CC = 0, CG = 0.107142857, CT = 0, GA = 0.069444444, GC = 0.022222222, GG = 1, GT = 0.016129032, TA = 0, TC = 0, TG = 0.038961039, TT = 0) 3 All possible mismatches have been captured in the table. For each base, there are 3 possible type of mismatches. FYI, rU:dA, rG:dC, rC:dG and rA:dT are all considered matches. Best regards, Julie
ADD COMMENTlink modified 6 weeks ago • written 6 weeks ago by Julie Zhu3.8k
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