# The MEME Suite

## Motif-based sequence analysis tools

## tamo2meme

### Usage:

`tamo2meme [options] <TAMO file>`

### Description

Convert a TAMO file into a MEME motif file suitable for use with MEME Suite programs.

### Input

#### TAMO File

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.

### Output

### Options

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

### Example TAMO file

    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