Question: motif scanning using position frequncy matrix of motif in a given set of DNAstringset sequnces?.
gravatar for vinod.acear
4.1 years ago by
vinod.acear40 wrote:

Hi I have given set of sequences as DNAstringset and  position frequncy matrix of desired motif, out of these sequences some of them have  only one desired motif  in them at different location ( unkown). Please suggest me the method, to find highest scoring motif location in the DNAstringset sequences.

ADD COMMENTlink modified 4.1 years ago • written 4.1 years ago by vinod.acear40

Hello vinod.acear!

Questions similar to yours can already be found at:


ADD REPLYlink modified 4.0 years ago • written 4.0 years ago by Hervé Pagès ♦♦ 14k

Hi Herve i used MEME server to discover motif PFM (position frequency matrix) but now i need to use that motif to scan this type of motif on other set of sequences.Note: Both Problems are different. Till now i have used matchPWM of but it is not giving highest scoring match and giving multiple Motif on scan a sequence.  

ADD REPLYlink written 4.0 years ago by vinod.acear40

True. Sorry for that. I re-opened your question.


ADD REPLYlink written 4.0 years ago by Hervé Pagès ♦♦ 14k
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