Description

Meme is designed to discover motifs (highly conserved regions) in groups of related DNA or protein sequences, and Mast will search sequence databases using motifs. Meme & Mast were developed at UCSD and Purdue. Meme/Mast website.

Meme is cpu-intensive for large numbers of sequences or long sequences. As a rule of thumb, if you run meme and get the error:

Dataset too large (> 100000). Rerun with larger -maxsize.

you should use the parallel version of Meme that is available on Biowulf.

By default, Meme and Mast create html output. For text output, use the '-text' parameter.

Meme and Mast have online documentation. To see the available parameters, run 'meme' or 'mast' with no parameters.

Version

The output of Meme and Mast include the version number at the top of the output.

Sample session

(user input in bold):

[user@helix mydir]$ meme -text protease-seqs > protease.meme.out
Initializing the motif probability tables for 2 to 7 sites...
nsites = 7
Done initializing

seqs=     7, min= 185, max=  300, total=     1750

motif=1
em: w=  50, psites=   7, iter=   0  

[user@helix mydir]$ mast protease.meme.out -text
Writing to file mast.protease.meme.out

[user@helix mydir]$ more mast.protease.meme.out
********************************************************************************
MAST - Motif Alignment and Search Tool
********************************************************************************
        MAST version 3.5.7 (Release date: 2007-12-17 16:56:19 -0800
	(Mon, 17 Dec 2007))
[...]
********************************************************************************
DATABASE AND MOTIFS
********************************************************************************
        DATABASE protease-seqs (peptide)
        Last updated on Wed Feb 20 09:46:42 2008
        Database contains 7 sequences, 1750 residues

        MOTIFS protease.meme.out (peptide)
        MOTIF WIDTH BEST POSSIBLE MATCH
        ----- ----- -------------------
          1    50   VIRRGSTTGTHSGRVTALNATVNYGGGDVVYGMIQTNVCAEPGDSGGPLY
[...]

For a full explanation of the Meme and Mast output, see Meme output and Mast output in the documentation.

Documentation

1. Type 'meme' or 'mast' with no parameters on the command line to see a list of all available options and more information.
2. Meme documentation at the SDSC website.
3. Mast documentation at the SDSC website.