transfac2meme
Usage: transfac2meme [options] <matrix file>
Description:
Extract motifs from a transfac 'matrix.dat' file and print them in MEME Version 3.0 format.
Counts are converted to frequencies using pseudo-counts determined by the backgoround frequencies and the total pseudocounts (see -bg and -pseudo, above). The log-odds matrix uses the background frequencies in the denominator and is log base 2.
N.B. Dollar signs in TRANSFAC IDs are converted to underscores.
Input:
A file in TRANSFAC matrix format
Options:
-
-numbers
Print numbers instead of names as motif IDs. -
-use_acc
Use and print accession names instead of IDs. -
-species <name>
Extract only motifs for this species. -
[-skip <ID>]*
IDs to skip -
-ids <idfile>
File with TRANSFAC IDs, one per line -
-bg <bfile>
File with background frequencies in MEME background file format; default: uniform frequencies -
-pseudo <A>
Add <A> times background frequency to each count when computing letter frequencies default: 1
Output
Writes MEME format to standard output.