matrix2meme [options]


Convert count or frequency matrices separated by empty lines into MEME motifs.


Count/Frequency Matrices

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.
-alphalphabet file Use the alphabet defined in the file. The DNA alphabet is used.
-orienauto|col|row Set the matrix orientation. The matrix orientation is automatically detected.
-numseqscount Assume frequences based on count sequence sites. The motif is created as if it was made from 20 sequence sites.