This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Python Script For Exact P-Value Of Pwm

Hi guys,

I am looking for native python or perl scripts for the calculation of score threshold for Position weight matrix (PWM) given a p-value. The ideal will be a function, that given a matrix in jasapr/transfac format and a p-value, will return the score for that p-value.

Sure, I can try and build the algorithm myself, but I will be glad if some one already did it.

p-value p-value p-value p-value
• 5,025 views • link
updated by Biostar Biostar • written by Dror • Dror

funny, when I try to edit this, I see only one green flashing tag, what is that for, merged tags?

• 0 views • link
written by Michael Dondrup Michael Dondrup

I see it too. Maybe the browser is rendering the same tag 4 times producing the flashing effect.

• 0 views • link
written by Damian Kao Damian Kao

1 answer

You can use MOODS. It has a biopython interface.

The BioPython interface has a threshold_from_p function

• 105 views • link
written by Damian Kao Damian Kao

+1. Hadn't seen MOODS before. Thanks for this @DK.

• 0 views • link
written by Casey Bergman Casey Bergman

Log in to answer this question.

More posts like this