Question: PWM matching alogrithm
1
gravatar for zhenyisong
5.8 years ago by
zhenyisong130
China
zhenyisong130 wrote:

I want to optimize the PWM algorithm. My original approach is brute force strategy which each position PWM score is calculated and compared with the threshold.Thus the running time is exponential dependent on the length of input string (DNA fragment). Is there some kind of speeding method to improve the performance the PWM string matching? If available, please provide some papers related to this problem so that I can implemented in my task. Thanks in advance.

motif pwm ;dna alogrithm; • 2.0k views
ADD COMMENTlink modified 4.7 years ago by ibarra.ignacio10 • written 5.8 years ago by zhenyisong130
1
gravatar for ibarra.ignacio
4.7 years ago by
ibarra.ignacio10 wrote:

I would suggest MOODS. It implements an algorithmic improvement to the classic PWM scanning, to find motif matches in linear time. http://www.cs.helsinki.fi/group/pssmfind

HTH!

ADD COMMENTlink modified 9 months ago by RamRS30k • written 4.7 years ago by ibarra.ignacio10
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