Is there any paper about motif finding based on PWM on genome sequence?

Question

[bharata1803]

Hello,

I have a PWM data. I want to scan it to genome to know the occurence and predict the transcription factor - target gene relationship. I know tools like PWMScan. I want to use the same tools but offline. Is there any suggestion? I also want to learn how to make it myself, probably by python or Java. Is there any suggestion about paper to read so to use PWM to find motif and the statistic to determine the significance of the findings? Thank you.

Answer 1

[natasha.sernova]

See this post:

How to query for a specific motif upstream of each of the gene in a list?

and this paper:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4763482/

But I think the post should be enough.