transfac2meme [options] <matrix file>


Convert a TRANSFAC 'matrix.dat' file into a MEME motif file suitable for use with MEME Suite programs.


TRANSFAC matrix File

A file in TRANSFAC matrix format of in a "TRANSFAC-like" format.

The IUPAC letter at the end of each matrix line is optional. The motif name is taken from the "ID" line, but may also be taken from the "AC" or "NA" line if requested using an optional parameter (below). The "NA" name, if present, is used as the secondary motif name, separated by a space from the primary name, except when it is requested to be the primary name. Note that dollar signs are converted to underscores in the motif name.

Each TRANSFAC(-like) entry must end with either an "XX" or "//" line.



Option Parameter Description Default Behaviour
General Options
-use_acc Use the accession name instead of the TRANSFAC ID as the motif identifier.
-idsID file Keep only the motifs identified in the ID file. Keep all motifs.
-speciesspecies name Keep only motifs with this species name. Keep all motifs.