jaspar2meme [options] <jaspar directory>
Convert a directory of JASPAR files into a MEME motif suitable for use with MEME Suite programs.
A directory containing one or more JASPAR motif files in one of three formats.
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.
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.
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.
| 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). |
|
| -strands | 1|2 | Specify if a single strand or both strands were considered to create the motif. | Defaults to reporting that both strands were scanned. |
>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 ]
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
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