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.
| Option | Parameter | Description | Default Behaviour |
|---|---|---|---|
| General Options | |||
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