Comparing position weight matrices

Question

[anshupa.vssut]

Hello All,

I have my sequences represented as position weight matrix and wish to check for transcription factors occurring in those sequences. Can anyone suggest a tool that compares position weight matrices?

[Santosh Anand]

I am afraid that if you represent all the sequences with PWM, it will dilute the actual signal of TFBS. The usual way is to start from the sequences and look for de-novo, or otherwise known motifs. Meme suite has different kind of tools for every need http://meme-suite.org/

[anshupa.vssut]

I have already performed this analysis. I am currently looking for methods to handle short sequences of length upto 30 bp which are enriched for SNVs but are not identified by FIMO. For that, I represent these short sequences as position weight matrix(PWM) and intend to compare this with existing PWMs of transcription factors.