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Oct
12
comment Scoring sequence against position weight matrix
let us continue this discussion in chat
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