# Background model format

The format for n-order Markov background models is as follows.

The file must contain one line for each combination of 1, 2, ..., n-1 letters in the alphabet. The DNA alphabet is ACGT and protein the protein alphabet is ACDEFGHIKLMNPQRSTVWY.

Each line must contain the letter combination followed by the letter combination's frequency (probability). All other lines in the file are ignored, including comment lines starting with '#'.

For example, a 0-order Markov model <file> might contain:

    # tuple   frequency_non_coding
    a       0.324
    c       0.176
    g       0.176
    t       0.324

A 1-order Markov model <file> might contain:

    # tuple   frequency_non_coding
    a       0.324
    c       0.176
    g       0.176
    t       0.324
    # tuple   frequency_non_coding
    aa      0.119
    ac      0.052
    ag      0.056
    at      0.097
    ca      0.058
    cc      0.033
    cg      0.028
    ct      0.056
    ga      0.056
    gc      0.035
    gg      0.033
    gt      0.052
    ta      0.091
    tc      0.056
    tg      0.058
    tt      0.119

NOTE: You can create a background model file from any FASTA sequence file using the `fasta-get-markov` command.