% This HMM is a four-M-state null model (equal transition probabilities
% and equal amino acid prbabilities across all acid type and across
% all M-states).
%
% Scott F. Smith
% Department of Electrical and Computer Engineering
% Boise State University
% SFSmith@BoiseState.edu
%
% 12 March 2004


% Transition probabilities D(1)-D(2), D(2)-D(3), ... , D(N-1)-D(N)
% There should be N-1 of these
DDtrans = [ ...
1/3 1/3 1/3
];

% Transition probabilities BEG-M(1), M(1)-M(2), ... , M(N)-END
% There should be N+1 of these
MMtrans = [ ...
1/3 1/3 1/3 1/3 1/2
];

% Transition probabilities I(0)-I(0), I(1)-I(1), ... , I(N)-I(N)
% There should be N+1 of these
IItrans = [ ...
1/3 1/3 1/3 1/3 1/2
];

% Transition probabilities D(1)-M(2), D(2)-M(3), ... , D(N)-END
% There should be N of these
DMtrans = [ ...
1/3 1/3 1/3 1/2
];

% Transition probabilities BEG-D(1), M(1)-D(2), ... , M(N-1)-D(N)
% There should be N of these
MDtrans = [ ...
1/3 1/3 1/3 1/3
];

% Transition probabilities I(0)-D(1), I(1)-D(2), ... , I(N-1)-D(N)
% There should be N of these
IDtrans = [ ...
1/3 1/3 1/3 1/3
];

% Transition probabilities D(1)-I(1), D(2)-I(2), ... , D(N)-I(N)
% There should be N of these
DItrans = [ ...
1/3 1/3 1/3 1/2
];

% Transition probabilities I(0)-M(1), I(1)-M(2), ... , I(N)-END
% There should be N+1 of these
IMtrans = [ ...
1/3 1/3 1/3 1/3 1/2
];

% Transition probabilities BEG-I(0), M(1)-I(1), ... , M(N)-I(N)
% There should be N+1 of these
MItrans = [ ...
1/3 1/3 1/3 1/3 1/2
];

% Probabilities of each amino acid in each M-state
% There should be 20 columns and N rows
AcidProbs = [ ...
0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05
0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05
0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05
0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05
];

% Number of M-states in the HMM
N = length(DMtrans);