transfac2meme [options] <matrix file>
Convert a TRANSFAC 'matrix.dat' file into a MEME motif file suitable for use with MEME Suite programs.
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.
Writes MEME motif format to standard output.
A probability matrix and optionally a log-odds matrix are output for each motif in the file. The probability matrix is computed using pseudo-counts consisting of the background frequency (see -bg, below) multiplied by the total pseudocounts (see -pseudo, below). The log-odds matrix uses the background frequencies in the denominator and is log base 2.
| Option | Parameter | Description | Default Behaviour |
|---|---|---|---|
| General Options | |||
| -numbers | Use a number based on the position in the input instead of the TRANSFAC ID as the motif identifier. | The TRANSFAC ID is used as the motif identifier. | |
| -use_acc | Use the accession name instead of the TRANSFAC ID as the motif identifier. | The TRANSFAC ID is used as the motif identifier. | |
| -ids | ID file | Keep only the motifs identified in the ID file. | Keep all motifs. |
| -species | species name | Keep only motifs with this species name. | Keep all motifs. |
| -skip | ID | Skip the motif identified by ID. This option can be repeated to skip more than one motif. | Motifs are not skipped. |
| -bg | background file | The background file should be a Markov background model. It contains the background frequencies of letters use for assigning pseudocounts. The background frequencies will be included in the resulting MEME file. | Uses uniform background frequencies. |
| -pseudo | total pseudocounts | Add total pseudocounts times letter background to each frequency. | No pseudocount is added. |
| -logodds | Include a log-odds matrix in the output. This is not required for versions of the MEME Suite ≥ 4.7.0. | The log-odds matrix is not included in the output. | |
| -url | website | The provided website URL will be stored with the motif and this can be used by MEME Suite programs to provide a direct link to that information in their output. If website contains the keyword MOTIF_NAME the TRANSFAC ID is substituted in place of MOTIF_NAME in the output. For example if the url is http://big-box-of-motifs.com/motifs/MOTIF_NAME.html and the TRANSFAC ID is M0001, the motif will contain a link to http://big-box-of-motifs.com/motifs/M0001.html Similarly, the TRANSFAC accession number is substituted for MOTIF_AC and the TRANSFAC ID is substituted for MOTIF_ID in the URL string. | The output does not include a URL with the motifs. |