motif scanning using position frequncy matrix of motif in a given set of DNAstringset sequnces?.
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vinod.acear ▴ 50
@vinodacear-8884
Last seen 17 months ago
India

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.

motifdb matchpwm motif pwmenrich pwm • 946 views
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Hello vinod.acear!

Questions similar to yours can already be found at:

H.

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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.  

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

H.

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