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Oct
12
comment Scoring sequence against position weight matrix
let us continue this discussion in chat
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
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
comment Scoring sequence against position weight matrix
I edited my question with an example. See above ^