Question: MEME-FIMO return different count of target for the same sequence
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3.2 years ago by
14061048890
14061048890 wrote:

Hi, I have a motif of 48bp which is presented by a letter-probability matrix. I scanned this motif using the FIMO program of MEME suite in a DNA sequence which length is about 600Mb and some other smaller subsequences truncated from the prior huge sequence. But I got different target numbers in the subsequences and the same regions in the huge sequence. I used default parameters for running the FIMO program. I would much appreciate if you could kindly help me.

meme fimo motif-scan • 694 views
ADD COMMENTlink written 3.2 years ago by 14061048890

I think your background model will be different for whole genome and its fragments. And that might be the reason for the differences in motif detection.

ADD REPLYlink written 3.2 years ago by Satyajeet Khare1.6k
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