jaspar2meme

Usage:

jaspar2meme [options] <jaspar directory>

Description

Convert a directory of JASPAR files into a MEME motif suitable for use with MEME Suite programs.

Inputs

JASPAR Directory

A directory containing one or more JASPAR motif files in one of three formats.

JASPAR Sites Format

This format describes a motif in terms of a multiple alignment of sites. It contains a multiple alignment in modified FASTA format. Only capitalized sequence letters are part of the alignment. The sites formatted files are expected to end with the .sites extension.

JASPAR Count Format

This format describes a motif in terms of a count matrix where the rows correspond to A, C, G and T respectively. The JASPAR count files are expected to end with the .pfm extension.

CM Count Format

This format describes a motif in terms of a count matrix with each row preceeded by the letters A|, C|, G| and T|. The CM count files are expected to end with the .cm extension.

Outputs

Options

Option Parameter Description Default Behaviour
General Options
-pfm Read JASPAR count files (.pfm). Read JASPAR site files (.sites).
-cm Read count files (.cm) with line labels A| etc. Read JASPAR site files (.sites).
-strands1|2 Specify if a single strand or both strands were considered to create the motif. Defaults to reporting that both strands were scanned.

Example Input Formats

JASPAR Sites Format Example

>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 ]
      

JASPAR Count Format Example

 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 Count Format Example

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