tamo2meme [options] <TAMO file>
Convert a TAMO file into a MEME motif file suitable for use with MEME Suite programs.
A TAMO file describes one or more motifs in terms of a Log-odds matrix and a set of sites that were used to make the motif. The script reads the sites and converts them into a position specific probability matrix.
See the example.
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 | |||
| -skip | ID | Skip the motif identified by ID. This option can be repeated to skip more than one motif. | Motifs are not skipped. |
| -numbers | Use a number based on the position in the input instead of the TAMO ID as the motif identifier. | The TAMO ID is used as the motif identifier. | |
| -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 TAMO ID is substituted in place of MOTIF_NAME in the output. For example if the url is http://big-box-of-motifs.com/motifs/MOTIF_NAME.html and the TAMO ID is tamo_id, the motif will contain a link to http://big-box-of-motifs.com/motifs/tamo_id.html | The output does not include a URL with the motifs. |
Log-odds matrix for Motif 0 rGAA..TtctrGAA (0)
# 0 1 2 3 4 5 6 7 8 9 10 11 12 13
#A 0.743 -1.052 1.647 1.443 -1.558 -0.374 -3.255 -5.001 -0.793 -2.480 1.175 -3.678 1.635 1.629
#C -1.105 -10.336 -8.324 -3.641 0.691 0.311 -1.463 -0.208 1.931 -1.053 -2.000 -10.641 -2.819 -4.350
#T -3.868 -3.114 -4.032 -2.297 0.288 -0.426 1.428 1.320 -2.576 1.393 -5.066 -3.566 -5.030 -3.764
#G 0.967 2.100 -4.305 -1.267 0.140 0.632 -1.563 -1.879 -2.088 -2.285 0.357 2.321 -8.368 -4.399
Sequence Logo
# --------------
# -- 2.30 bits
# G
# G
# GA GAA
# GAA T C GAA
# GAA TTCT GAA
# AGAA TTCTAGAA
# GGAA TTCTAGAA -- 0.29 bits
# --------------
# rGAA..TtctrGAA
Source: HSF1
Motif 0 rGAA..TtctrGAA (0) (Bits: 14.14 MAP: 0.00 D: 0.000 -1) E: 0.000 ch: 0.00
AAAAAACCAAAGAA 0 2.66564019036
AAAACACCACAGAA 0 6.34181478692
AGAACAGCCCAGAA 0 12.1162311612
AGAACCGCCGAGAA 0 11.5694520088
AGAACCTCCGAGAA 0 14.5611965064
AGAACCTGCTAGAA 0 16.5680637894
AGAACCTTCTAGAA 0 19.7669118865
AGAACCTTCTAGAA 0 19.7669118865
CGAACCTTCTAGAA 0 17.9190181888
CGAAGGTTCTAGAA 0 17.6896096981
GGAAGGTTCTAGAA 0 19.761489259
GGAAGGTTCTAGAA 0 19.761489259
GGAAGGTTCTCGAA 0 16.5861453685
GGAAGGTTCTGGAA 0 18.9435955025
GGAAGGTTCTGGAA 0 18.9435955025
GGAATGTTCTGGAA 0 19.0918355924
GGACTGTTCTGGAA 0 14.0084990288
GGAGTTTTCTGGAA 0 15.32449778
GGAGTTTTCTGGAA 0 15.32449778
GGATTTTTGTGGCC 0 -0.158188860768
**************
MAP Score: 0.000000