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 4.3 years 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 • 1.6k views

ADD COMMENT • link 9.1 years ago vinod.acear ▴ 50

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Hello vinod.acear!

Questions similar to yours can already be found at:

Please suggest any good motif Discovery tool in R-Bioconductor.

H.

ADD REPLY • link 9.1 years ago Hervé Pagès 16k

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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.