beeml2meme [options] <matrix file>+
Convert one or more BEEML matrix files into a MEME motif file suitable for use with MEME Suite programs.
One or more BEEML matrix files describing one or more motifs in terms of letter energy values.
# cell08_Alx3_3418, probe_r_sqr = 0.676, 8mer_r_sqr = 0.868
A 0.12 1.48 0 0 2.18 1.15 0 0.09 0.14 0.13
C 0.02 1.69 1.57 2.2 1.7 0.99 0.82 0.36 0 0.27
G 0.42 2.31 1.9 2.8 2.3 1.12 0.16 0 0.25 0.27
T 0 0 1.67 1.62 0 0 0.59 0.52 0.04 0
# cell08_Alx4_1744, probe_r_sqr = 0.756, 8mer_r_sqr = 0.895
A 0 0.73 0.97 0 0 3.35 2.65 0 0 0.25
C 0.36 0 0 1.58 2.82 3.82 2.23 3.44 0.67 0
G 0.16 0.5 1.32 1.86 2.94 6.2 2.42 3.01 0.21 0.11
T 0.25 0.15 0.05 1.59 3.23 0 0 1.98 0.31 0.28
Writes MEME motif format to standard output.
A probability matrix and optionally a log-odds matrix are output for each motif in the 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). The log-odds matrix uses the background frequencies in the denominator and is log base 2.
| Option | Parameter | Description | Default Behaviour |
|---|---|---|---|
| General Options | |||
| -bg | background file | The background file should be a Markov background model. It contains the background frequencies of letters use for assigning pseudocounts. The background frequencies will be included in the resulting MEME file. | Uses uniform background frequencies. |
| -pseudo | total pseudocounts | Add total pseudocounts times letter background to each frequency. | No pseudocount is added. |
| -logodds | Include a log-odds matrix in the output. This is not required for versions of the MEME Suite ≥ 4.7.0. | The log-odds matrix is not included in the output. | |
| -url | website | The provided website URL will be stored with the motif and this can be used by MEME Suite programs to provide a direct link to that information in their output. If website contains the keyword MOTIF_NAME the Uniprobe ID # is substituted in place of MOTIF_NAME in the output. For example if the url is http://the_brain.bwh.harvard.edu/uniprobe/details2.php?id=MOTIF_NAME and the Uniprobe ID # is 00419, the motif will contain a link to http://the_brain.bwh.harvard.edu/uniprobe/details2.php?id=00419 | The output does not include a URL with the motifs. |
| -sg | Uniprobe screen grab | Use the screen grab of the Uniprobe browser http://the_brain.bwh.harvard.edu/uniprobe/browse.php to assign Uniprobe IDs to BEEML IDs. | The BEEML matrics must already contain a Uniprobe ID directly following the BEEML ID or the URL will not be added to the motifs. |