# The MEME Suite

## Motif-based sequence analysis tools

## MEME Dirichlet Mixtures Format

### Description

A Dirichlet mixture file specifies residues' tendencies to align with one another, and is the basis for scoring columns of aligned residues in MEME and GLAM2.

### Format Specification

The format is identical to that of the UCSC Dirichlet mixtures. The default 30-component mixture prior used by MEME is given here.

## GLAM2 Dirichlet Mixtures Format

The GLAM2 programs use the same format as MEME but only read lines beginning with Mixture= or Alpha=. Mixture= is followed by a number giving the weight of that mixture component: these weights should sum to 1. Alpha= is followed by a list of numbers giving the pseudocounts for that mixture component, as many as there are symbols in the alphabet. The first number after Alpha= is the sum of the pseudocounts, and is in fact ignored by the GLAM2 programs.

The pseudocounts should be in the same order as the alphabet symbols. For the n (nucleotide) alphabet, this is: acgt. For the p (protein) alphabet, this is: ACDEFGHIKLMNPQRSTVWY.

If no Dirichlet mixture file is specified, the GLAM2 programs use recode3.20comp for the p (protein) alphabet, glam_tfbs.1comp for the n (nucleotide) alphabet, and a uniform prior for user-specified alphabets.