matrix2meme [options]
Convert count or frequency matrices separated by empty lines into MEME motifs.
Reads matrices from standard input separated by empty lines.
Example DNA count matrix:
1 5 6 3 5 5 5 0 12 1 1 1
The motifs are named based on their order in the file but their consensus sequence is used as the alternate name.
| Option | Parameter | Description | Default Behaviour |
|---|---|---|---|
| General Options | |||
| -dna | Use the DNA alphabet. Note that this is actually the default. | The DNA alphabet is used. | |
| -protein | Use the protein alphabet. | The DNA alphabet is used. | |
| -alph | alphabet file | Use the alphabet defined in the file. | The DNA alphabet is used. |
| -orien | auto|col|row | Set the matrix orientation. | The matrix orientation is automatically detected. |
| -numseqs | count | Assume frequences based on count sequence sites. | The motif is created as if it was made from 20 sequence sites. |