Re: The motif match in a reverse complement way

[CharlesEGrant]

When people determine the DNA binding sites and define the DNA binding motifs, do they consider the gene transcriptional direction?

It depends on the experiments that generated the motifs.  In ChIP-Seq experiments the relevant genes may not even be known! By default MEME considers the input sequences in both senses but you can turn on an option to only consider the forward sense. The forward and reverse complement versions of a motif are really just different representations of the same underlying sequence of base pairs. In the absence of other information a TomTom match to a motif in the RC representation is just as significant as a match to the forward representation.

[fortu...@gmail.com]

Thank you for your reply. This makes me think that when people mention DNA motifs in their research, they may always need to mention the reverse strand is also possible. However, what I saw in the literature only gave one sequence. I think there should be a standard in this field to eliminate unnecessary confusions.