scpd2meme [options] <matrix file>
Convert an SCPD matrix file into a MEME motif suitable for use with MEME Suite programs.
An SCPD matrix file describes one or more motifs in terms of letter frequencies.
>RLM1 22 524 MCB 1997, 17:1848-1859
A 10 14 11 0 0 0 42 16 22 23 32 0 42 0 27 4 7 10
T 8 10 30 37 0 42 0 26 20 19 10 42 0 0 1 20 16 7
G 10 16 1 5 0 0 0 0 0 0 0 0 0 42 0 2 3 10
C 10 2 0 0 42 0 0 0 0 0 0 0 0 0 14 15 16 13
>SMP1 11 405 MCB 1997, 17:1848-1859
A 8 8 11 0 0 8 0 0 30 6 13 14 21 0 30 2 8 27 9 6
T 4 12 0 9 30 11 1 30 0 24 16 16 9 30 0 0 7 1 9 7
G 5 4 19 0 0 11 0 0 0 0 0 0 0 0 0 28 0 0 7 4
C 3 5 0 21 0 0 29 0 0 0 0 0 0 0 0 0 14 0 4 9
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 | |||
| -skip | ID | Skip the motif identified by ID. This option can be repeated to skip more than one motif. | Motifs are not skipped. |
| -numbers | Use a number based on the position in the input instead of the SCPD ID as the motif identifier. | The SCPD ID is used as the motif identifier. | |
| -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 SCPD 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 SCPD ID is scpd_id, the motif will contain a link to http://big-box-of-motifs.com/motifs/scpd_id.html | The output does not include a URL with the motifs. |