iupac2meme

Usage: iupac2meme [options] [<iupac_motif>]+

Description:

Convert an IUPAC motif into a MEME version 4 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. This program additionally supports regular expression bracket expressions where multiple letters can be grouped in one with the use of square brackets.

A background frequency file modifies the assumption of equal probability of all alternative letters.

A probability matrix and optionally a log-odds 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; default: uniform background

-pseudo <total pseudocounts>

add <total pseudocounts> times letter background to each frequency; default: 0

-logodds

output the log-odds (PSSM) and frequency (PSPM) motifs; default: PSPM motif only

-url <website>

website for the motif; The motif name is substituted for MOTIF_NAME; default: no url

Output:

Writes MEME format to standard output.

Sample Input:

DNA IUPAC motif:

  ACGGWN[ACGT]YCGT

protein IUPAC motif:

  IKLVBZYXXHG