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Hi
I have a question on meme motif discovery and strand of the sequence.
When discovering motifs does MEME considers by default both forward and reverse strands of a given input sequence? I read in it in this https://groups.google.com/forum/#!to...te/1bTc2sDBqZU that MEME considers both forward and reverse strand when discovering motif (assuming they were taking about motif discovery and not pattern matching because I can see in pattern matching MAST does consider both strands).
Also if the above is true then why does the MEME motif discovery manual gives an option for -revcomp.
As described in under this option:
when given -revcomp Consider both the given strand and the reverse complement strand when searching for motifs in a complementable alphabet (ie DNA).
by default- Search for motifs of complementable alphabets on the given strand only.
Please clarify.
I have a question on meme motif discovery and strand of the sequence.
When discovering motifs does MEME considers by default both forward and reverse strands of a given input sequence? I read in it in this https://groups.google.com/forum/#!to...te/1bTc2sDBqZU that MEME considers both forward and reverse strand when discovering motif (assuming they were taking about motif discovery and not pattern matching because I can see in pattern matching MAST does consider both strands).
Also if the above is true then why does the MEME motif discovery manual gives an option for -revcomp.
As described in under this option:
when given -revcomp Consider both the given strand and the reverse complement strand when searching for motifs in a complementable alphabet (ie DNA).
by default- Search for motifs of complementable alphabets on the given strand only.
Please clarify.
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