jaspar2meme [options] <file_name | directory_name>
Convert a file of motifs in JASPAR 2014 or 2016 PFM format or a directory of JASPAR files in one of the three old JASPAR formats (SITES, PFM or CM) into a MEME motif suitable for use with MEME Suite programs.
file_nameThe file contains motifs in JASPAR 2014 or 2016 PFM format. In these formats, each motif is preceded by a header line that begins with '>' and is followed by a unique identfier (e.g., 'MA0001.1'). An optional second identifier can follow the first (e.g., 'SEP4'). JASPAR 2016 PFM format includes the letter at the beginning of each line and square brackets around the line of counts.
directory_nameA directory containing one or more JASPAR motif files in one of the following three formats.
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
file names are expected to end with the .pfm extension.
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 file names
are expected to end with the .sites 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 file names are expected
to end with the .cm extension.
| Option | Parameter | Description | Default Behaviour |
|---|---|---|---|
| General Options | |||
| -bundle | Read motifs in JASPAR 2014 or JASPAR 2016 PFM format from the file named file_name.
The lines may be in any order but the MEME matrices will be output with
the lines in the standard order (e.g., ACGT for DNA). |
Read JASPAR SITES files (.sites) from directory_name. |
|
| -pfm | Read JASPAR PFM files (.pfm) from directory_name. |
Read JASPAR SITES files (.sites) from directory_name. |
|
| -cm | Read JASPAR CM files (.cm) with line labels A| etc.
from directory directory_name. |
Read JASPAR SITES files (.sites) from directory_name. |
|
| -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. |
>MA0002.1 RUNX1
10 12 4 1 2 2 0 0 0 8 13
2 2 7 1 0 8 0 0 1 2 2
3 1 1 0 23 0 26 26 0 0 4
11 11 14 24 1 16 0 0 25 16 7
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
>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 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