[BiO BB] PWM search tool

Ryan Golhar golharam at umdnj.edu
Wed Feb 7 19:28:39 EST 2007

You could use prophecy/profit from the EMBOSS suite.  As for a threshold,
try calculating the relative score (Absolute score - Min Score)/(Max Score -
Min Score) - 100%, where absolute score is the score given by the matrix,
and min score is the smallest possible score from the matrix and max score
is the maximum possible score.  That should tell you how good the score is
for any given alignment from the matrix.


Ryan Golhar, PhD
Informatics Institute of UMDNJ
golharam at umdnj.edu

> -----Original Message-----
> From: 
> bio_bulletin_board-bounces+golharam=umdnj.edu at bioinformatics.o
> rg 
> [mailto:bio_bulletin_board-bounces+golharam=umdnj.edu at bioinfor
> matics.org] On Behalf Of Samantha Fox
> Sent: Wednesday, February 07, 2007 3:41 PM
> To: General Forum at Bioinformatics.Org
> Subject: [BiO BB] PWM search tool
> Hey !
> I am looking for a good tool on PWM search in DNA sequences. 
> Patser comes across as a popular one but I am uncertain about 
> the threshold score or p-value to use, to count PWM hits.
> Any views !
> ~S
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