Question: meme-suite: How does FIMO works?
gravatar for RT
6 months ago by
European Union
RT300 wrote:

Dear All,

I am new to motif identification area. From a set of sequences (~200), I want to search for a known motif and filter out sequences where the motif does not exist. My motif is 8bp long. A simple python search gave me too many random hits. Someone quickly suggested to me to use meme-tools and instead of simple pattern search use position-specific scoring matrix.

I think FIMO (from meme-suite) looks for known motif in given set of sequences. I ran it and it does not give me too many random hits. Python pattern search gave me as many as 9 hits on a 1000 bp long sequence. What I am struggling to understand is how FIMO works. How it calculates the log-odds scores on each sequence? Suggestions for any other tools are also welcome.

Thanks. RT

ADD COMMENTlink modified 4 months ago by Santosh Anand2.9k • written 6 months ago by RT300

You want an exact 8bp match?

ADD REPLYlink written 6 months ago by jrj.healey2.3k
gravatar for Santosh Anand
4 months ago by
Santosh Anand2.9k
Santosh Anand2.9k wrote:

Did you already look at FIMO documentation, which is very well documented

There you'll find link to paper also for details about score calculation

ADD COMMENTlink written 4 months ago by Santosh Anand2.9k
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