Jaspar

Jaspar transforms a directory of JASPAR files into a MEME version 4 patterned file fir for use with MEME Suite programs.

Input: a directory having one or more JASPAR motif files. The possible patterns are:

• A JASPAR ‘.sites’ file depicts a motif in terms of a multiple alignment of sites. It is comprised of a multiple alignment in modified FASTA format.
• A JASPAR count file (‘.pfm’) is comprised of a count matrix where the rows imply A, C, G and T, respectively.
• A CM count file (‘.cm’) prefixes the rows with ‘A| ‘, ‘C| ‘, ‘G| ‘ and ‘T| ‘.

A probability matrix and selectivelly a log-odds matrix is output for each motif file. The probability matrix is computed pseudo-counts containing of the background frequency (see -bg, below) multiplied by the total pseudocounts (see -pseudo, below).