nmica2meme [options]
Convert a nestedMICA (BioTiffin/XMS) matrix file into a MEME motif file suitable for use with MEME Suite programs.
Reads a nestedMICA (BioTiffin/XMS) matrix file from standard input.
See the Sample XMS file from Benos lab, University of Pittsburgh
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. |
| -numseqs | n | Assume frequences are based on n sites. | Assume frequences are based on 20 sites. |
| -truncate_names | Truncate the motif names (IDs) at the first underscore. | Use the full motif names. | |
| -numbers | Use a number based on the position in the input instead of the motif name as the motif identifier. | The motif name 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 motif name 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 motif name is Abd-B, the motif will contain a link to http://big-box-of-motifs.com/motifs/Abd-B.html | The output does not include a URL with the motifs. |
| -h | Outputs a brief usage message. | Runs as normal. | |