Omar
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 Oct12 comment Scoring sequence against position weight matrix Oct12 awarded Supporter Oct12 comment Scoring sequence against position weight matrix Well I see how the numbers make sense now. But my problem is rather getting my numbers to a 0-1 scale so that I can apply a cutoff in mind (maybe 0.8?) to filter peptides by the ones that bind better compared to the best match. I see how 10^-19 / 10^-12 would give me a number between 0 and 1. If I log2(10^-19 / 10^-12) I would get -23. Which essentially means there is 23 times less chance of my sequence occurring compared to the best. But my problem is mapping that value back to a probability 0-1 Oct12 comment Scoring sequence against position weight matrix Thanks. I am using amino acid sequences so I guess the background model would be (1/20)^15 then. I run into the problem when dividing the product of my score by the product of the best score since they are both very small numbers: for example 10^-19 / 10^-12 = 10^-7, which is indeed between 0 and 1 but it does not give me a sense of how similar it is to the best. What I am looking to score is how well some peptide matches a PWM (ranging from 0 to 1). Does this make sense? Appreciate the help Oct12 comment Scoring sequence against position weight matrix Also, if I have real life background probabilities (i.e. determined from a large database) would I just take the product of everything? Oct12 comment Scoring sequence against position weight matrix Thank you for that detailed answer! I am trying to get scored between 0 and 1 (i.e. a probability). I thought about taking the ratio of the score to the best match to the PWM. I'm guessing from what you just explained, I would have to divide by 0.004 for the sequence score and the best score. So using the score from BAAC : (0.072/0.004)/(0.18/0.004)? Would this work? Oct12 revised Scoring sequence against position weight matrix edited body Oct11 comment Scoring sequence against position weight matrix He is assuming by Msij he means the log(frequency/background.frequency). I dont have the frequency matrix. Just the probabilities. Oct11 awarded Editor Oct11 comment Scoring sequence against position weight matrix I edited my question with an example. See above ^ Oct11 revised Scoring sequence against position weight matrix added 525 characters in body Oct11 awarded Student Oct11 asked Scoring sequence against position weight matrix