iupac2meme
Usage: iupac2meme [options] [<iupac_motif>]+
Description:
Convert an IUPAC motif into a MEME version 3 formatted file suitable for use with MAST and other MEME Suite programs.
Input:
An IUPAC motif represents frequencies by using either an exact letter meaning that letter occurs in all sites, or ambiguous letters, representing an equal frequency of all the letters representing by that letter.
A background frequency file modifies the assumption of equal probability of all alternative letters.
A log-odds matrix and a probability matrix are output for each motif provided on the command line. 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:
-alpha dna|protein
- IUPAC alphabet; default: DNA-numseqs <numseqs>
- assume frequencies based on this many sequences; default: 20-bg <background file>
- file with background frequencies of letters, {f_a}; default: uniform background-pseudo <total pseudocounts>
- add <total pseudocounts> times f_a to each frequency; default: 0-logodds
- output the log-odds (PSSM) and frequency (PSPM) motifs; default: PSPM motif only
Output:
Writes MEME format to standard output.
Sample Input:
DNA IUPAC motif:
ACGGWNNYCGT
protein IUPAC motif:
IKLVBZYXXHG