meme2meme

Usage:

meme2meme [options] [<meme motif file>]+

Description

Convert and merge multiple MEME formatted files into a single minimal meme format file.

Input

MEME Motif File

A motif file in one of the formats output by MEME or DREME.

Output

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 log-odds matrix uses the background frequencies in the denominator and is log base 2.

Options

Option Parameter Description Default Behaviour
Input/Output
-consensus Numeric names are swapped for a consensus of the motif (IUPAC in the case of DNA or RNA) using the following procedure on each motif column. 1) The letter frequencies are sorted in decreasing order. 2) Letters with frequencies less than half that of the maximum are discarded. 3a) If the remaining set of letters matches a symbol (including ambiguous symbols), that symbol is used. 3b) Otherwise, if the remaining set contains more than half the core symbols, the wildcard is used. 3c) Otherwise the (up to) three letters with highest frequencies are placed between regular expression brackets. The original names are used.
-numbersUse a number based on the position in the input instead of the original ID as the motif identifier.The original ID is used as the motif identifier.
-bgbackground fileThe background file should be a Markov background model. The background frequencies will be included in the resulting MEME file.Uses background in first specified motif file.
-logoddsInclude 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.
-urlwebsiteThe provided website URL will be stored with the motif (unless the motif already has a URL) 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 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 motif ID is motif_id, the motif will contain a link to
http://big-box-of-motifs.com/motifs/motif_id.html
The output does not include a URL with the motifs unless the original motif already had a URL.
-forceurl MEME motifs may already have URLs embedded but this option causes them to be replaced by the URL passed to -url. Existing URLs are kept.
-xalph Convert all motifs to use the same alphabet as specified in the first motif file. The alphabet specifed in the first motif file must contain a superset of all the core symbols in the other motif file alphabets. All motif files must use the same alphabet.