It would be very nice to have an alternative means to completely de novo motif detection. Instead of querying a massive space of all possible k-mers and bipartite motif configurations (several hundred thousand), it would be nice to be able to only gather IPD scores for the ~1000 motifs that have been previously identified in bacterial methylomes and are present in the REBASE database. Applying this option would greatly speed up the filtermotifs pipeline.
Feature request
It would be very nice to have an alternative means to completely de novo motif detection. Instead of querying a massive space of all possible k-mers and bipartite motif configurations (several hundred thousand), it would be nice to be able to only gather IPD scores for the ~1000 motifs that have been previously identified in bacterial methylomes and are present in the REBASE database. Applying this option would greatly speed up the filtermotifs pipeline.