jaspar2meme

Usage: jaspar2meme [options] <Jaspar directory>

Description:

Convert a directory of JASPAR files into a MEME version 3 formatted file suitable for use with MEME Suite programs.

Input:

<Jaspar directory> - a directory containing one or more JASPAR motif files. The possible formats are:

A a probability matrix are output for each motif 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).

Options:

Output:

Writes MEME format to standard output.

Sample Input:

.pfm format (counts):

 0  3 79 40 66 48 65 11 65  0
94 75  4  3  1  2  5  2  3  3
 1  0  3  4  1  0  5  3 28 88
 2 19 11 50 29 47 22 81  1  6

.cm format (counts):

A|  0  3 79 40 66 48 65 11 65  0
C| 94 75  4  3  1  2  5  2  3  3
G|  1  0  3  4  1  0  5  3 28 88
T|  2 19 11 50 29 47 22 81  1  6

.sites format (motif sites):

>MA0024 E2F     1
aTTTGGCGC
>MA0024 E2F     2
TTTGGCGC
>MA0024 E2F     3
TTTGGCGC
>MA0024 E2F     4
TTTGGCGC
>MA0024 E2F     5
TTTCGCGC
>MA0024 E2F     6
TTTCGCGC
>MA0024 E2F     7
TTTCGCGC
>MA0024 E2F     8
TTTGCCGC
>MA0024 E2F     9
TTTCCCGC
>MA0024 E2F     10
TTTGGCGG

A  [ 0  0  0  0  0  0  0  0 ]
C  [ 0  0  0  4  2 10  0  9 ]
G  [ 0  0  0  6  8  0 10  1 ]
T  [10 10 10  0  0  0  0  0 ]