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    Archive for September 11th, 2006

    Position Frequency Matrix to Position Weight Matrix (PFM2PWM)

    11th September 2006

    In the course of my current research, I was dealing with the TFBS (Transcription Factor Binding Sites) search. To perfrom the search, one needs position weight matrix (PWM) for each TFBS. When you refer to the TRANSFAC database of transcription factors (and matrices), you will get position frequency matrix (PFM), and will need to convert PFM into PWM.

    I did find a couple of conversion formulas, but that was quite an effort to figure out which one is correct – I had seen two different formula variations. Here I will share what I had found.
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    Posted in Bioinformatics | 25 Comments »