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