strand specific motif enrichment with AME

[Peter Stoilov]

Is it possible to direct AME to test for motif enrichment only on the supplied strand? I working with RNA binding proteins and searching for binding site enrichment on the complementary strand not only doesn't make sense, but may skew the results.

[James Johnson]

Currently AME only supports testing both strands. We do intend to add the capability to work only with the given strand (as well as with any custom alphabet) in the 4.11 release.