transfac2meme
Usage: transfac2meme [options] <matrix file>
Description:
Extract motifs from a TRANSFAC 'matrix.dat' file and print them in MEME Version 4 format.
Counts are converted to frequencies using pseudo-counts determined by the backgoround frequencies and the total pseudocounts (see -bg and -pseudo, below). 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
- use numbers instead of strings as motif names
- -use_acc
- use accession names instead of IDs
- -ids <idfile>
- keep any motifs listed in the file
- -species <name>
- keep only motifs for this species
- -skip <ID>
- skip this ID (may be repeated)
- -bg <background file>
- file with background frequencies of letters;default: uniform background
- -pseudo <total pseudocounts>
- add <total pseudocounts> times letter background to each frequency; default: 0
- -logodds
- print log-odds matrix, too; default: print frequency matrix only
- -url <website>
- website for the motif; The ID (or accession) is substituted for MOTIF_NAME; default: no url
Output
Writes MEME format to standard output.
Sample Input