Question

Python Script For Exact P-Value Of Pwm

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12.9 years ago

Dror ▴ 280

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 • 4.4k views

ADD COMMENT • link updated 9.8 years ago by Biostar 20 • written 12.9 years ago by Dror ▴ 280

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

ADD REPLY • link 11.2 years ago by Michael 55k

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

ADD REPLY • link 11.2 years ago by Damian Kao 16k

score 6 · Answer 1 · 2011-12-20

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12.9 years ago

Damian Kao 16k

You can use MOODS. It has a biopython interface.

The BioPython interface has a threshold_from_p function

ADD COMMENT • link 12.9 years ago by Damian Kao 16k

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

ADD REPLY • link 12.9 years ago by Casey Bergman 18k