priority2meme
Usage: priority2meme [options]
<matrix file>
Description:
Convert a PRIORITY file into a MEME version 3 formatted file suitable for use with MAST and other MEME Suite programs.
Input:
A PRIORITY file describes a motif in terms of a position weight matrix. A file with background frequencies in MEME background file format is also required.
A log-odds matrix and a probability matrix are output for the motif. The probability matrix is computed using pseudo-counts consisting of the background frequency (see -bg, below) multiplied by the total pseudocounts (see -pseudo, below). The log-odds matrix uses the background frequencies in the denominator and is log base 2.
Options:
-numbers
Use numbers instead of strings as motif IDs-bg
file with background frequencies in MEME background file format; default: uniform frequencies-pseudo <A>
add<A>
times background frequency to each count when computing letter frequencies default: 0
Output:
Writes MEME format to standard output.