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
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?