# The MEME Suite

## Motif-based sequence analysis tools

## sites2meme

### Usage:

`sites2meme [options] <directory of files containg sites>`

### Description

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

### Input

####

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

### Output

### Options

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