Question: Comparing position weight matrices
gravatar for anshupa.vssut
20 months ago by
anshupa.vssut50 wrote:

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?

ADD COMMENTlink modified 20 months ago by WouterDeCoster37k • written 20 months ago by anshupa.vssut50

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

ADD REPLYlink written 20 months ago by Santosh Anand4.6k

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.

ADD REPLYlink modified 20 months ago • written 20 months ago by anshupa.vssut50
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