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 Jun 23 awarded Popular Question Oct 12 comment Scoring sequence against position weight matrix Oct 12 awarded Supporter Oct 12 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 Oct 12 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 Oct 12 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? Oct 12 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? Oct 12 revised Scoring sequence against position weight matrix edited body Oct 11 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. Oct 11 awarded Editor Oct 11 comment Scoring sequence against position weight matrix I edited my question with an example. See above ^ Oct 11 revised Scoring sequence against position weight matrix added 525 characters in body Oct 11 awarded Student Oct 11 asked Scoring sequence against position weight matrix