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:

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

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

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