The MEME Suite

Convert a directory of files containing sites into a MEME motif file suitable for use with MEME Suite programs.

A directory which contains files of sites. A motif will be generated for each file with the expected file extension (default ".txt"). The motif will use the name of the file, minus the file extension, as the identifier.

Example Sites file

AAGGTCA
AAGGTCA
AAGGTCA
AAGGTCA
AAGGTCA
AAGGTCA
AAGGTCA
AAGGTCA
AAGGTCA
AAGGTCA
CGGGTCA
CGGGTCA
CGGGTCA
GGGGTCG

Option	Parameter	Description	Default Behaviour
General Options
-ext	file extension	The file extension (with '.') of the sites files. Any files without this extension will be ignored. The file name minus the extension will be used as the motif ID.	Files with the extension .txt will be used as sites files.
-map	ID mapping file	The ID mapping file contains space separated pairs of the motif ID and the motif name with one entry per line.	Only the motif IDs are used.
-protein		Expect all inputs to use the protein alphabet and produce protein motifs.	Expect all inputs to use the DNA alphabet and produce DNA motifs
-alph	file	Expect all inputs to use the alphabet defined in the file and produce motifs of the same alphabet.	Expect all inputs to use the DNA alphabet and produce DNA motifs