p-value confusion

[CharlesEGrant]

Originally posted by lrvandaalwyk 11 Aug 2008

I first need to say that bioinformatics is not my area of expertise. That being said, I have been using the programs MEME and MAST in my research for well over a year now; these programs have played a major part in my understanding of a viral transcription factor's binding site. I have read the associated articles with these programs, and although I feel that I understand the implications of the algorithms used, I do not understand how to implement on my own. My current frustration is in regards to the P-value associated with predicted sequences in the output file generated by MAST. I have been using these values as cutoffs for how reliable a predicted site is to be confirmed experimentally for quite some time now, but I don't understand how they are calculated. Is there a resource someone can point me to that states how to calculate this p-value? Can someone explain what information I need to be able to calculate these values (other than having a PWM, a sequence to search, and access to the MAST site, ha, ha,).
_________________
Lindsay Dresang 
Research Assistant 
Sugden Lab, UW-Madison

[CharlesEGrant]

Originally posted by memento: 16 Jan 2009:

lrvandaalwyk wrote:

I first need to say that bioinformatics is not my area of expertise. That being said, I have been using the programs MEME and MAST in my research for well over a year now; these programs have played a major part in my understanding of a viral transcription factor's binding site. I have read the associated articles with these programs, and although I feel that I understand the implications of the algorithms used, I do not understand how to implement on my own. My current frustration is in regards to the P-value associated with predicted sequences in the output file generated by MAST. I have been using these values as cutoffs for how reliable a predicted site is to be confirmed experimentally for quite some time now, but I don't understand how they are calculated. Is there a resource someone can point me to that states how to calculate this p-value? Can someone explain what information I need to be able to calculate these values (other than having a PWM, a sequence to search, and access to the MAST site, ha, ha,).

Timothy L. Bailey and Michael Gribskov, "Combining evidence using 
p-values: application to sequence homology searches", Bioinformatics, 
Vol. 14, pp. 48-54, 1998.