reverse complement sequence

[malayaranjan behera]

I am using the MEME web to find the motif of RNA binding protein in the HITS-CLIP sequencing. So, which motif sequence will I consider; the sequence shown as result or the reverse complement sequence ?

[cegrant]

MEME and STREME should recognize that the sequences are RNA and will only consider a single strand, that is it won't consider matches to the reverse-complement as it would by default for DNA.

[malayaranjan behera]

In order to do motif analysis we use complementary DNA sequences as input from HITS CLIP sequencing. So, in this context which motif sequence will I consider; the sequence shown as a result or the reverse complement sequence?

[cegrant]

Motifs are not stranded (proteins bind in major or minor grove, not to one strand or the other) so either form of the sequence is an unambiguous representation of the motif. By convention the forward sequence is usually the one reported. You are passing cDNA to the motif analysis, so if  you want to report the motif in terms of the forward direction of the underlying DNA you'd report the reverse complement form of the motif.