scpd2meme
Usage: scpd2meme [options] <matrix file>
Description:
Convert an SCPD matrix file into a MEME version 3 formatted file suitable for use with MAST and other MEME Suite programs.
Input:
An SCPD matrix file describes one ore more motifs in terms of letter frequencies.
A log-odds matrix and a probability matrix are output for each motif in the file. 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:
-skip <scpd ID>
skip this ID (may be repeated)-numbers
use numbers instead of strings as motif IDs-bg <background file>
file with background frequencies in MEME background file format; default: uniform frequencies-pseudo <
total pseudocounts> add <total pseudocounts> times each background frequency; default: 0
Output:
Writes MEME format to standard output.
Sample Input:
>RLM1 22 524 MCB 1997, 17:1848-1859 A 10 14 11 0 0 0 42 16 22 23 32 0 42 0 27 4 7 10 T 8 10 30 37 0 42 0 26 20 19 10 42 0 0 1 20 16 7 G 10 16 1 5 0 0 0 0 0 0 0 0 0 42 0 2 3 10 C 10 2 0 0 42 0 0 0 0 0 0 0 0 0 14 15 16 13 >SMP1 11 405 MCB 1997, 17:1848-1859 A 8 8 11 0 0 8 0 0 30 6 13 14 21 0 30 2 8 27 9 6 T 4 12 0 9 30 11 1 30 0 24 16 16 9 30 0 0 7 1 9 7 G 5 4 19 0 0 11 0 0 0 0 0 0 0 0 0 28 0 0 7 4 C 3 5 0 21 0 0 29 0 0 0 0 0 0 0 0 0 14 0 4 9