exp005 - Influenza Map Visualization


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function OUT_DATA=CalculateProteinEntropy(Ref, ALIGN_CELL)

OUT_DATA = cell(size(ALIGN_CELL));
for i = 1:size(ALIGN_CELL,1)

    aligned_seqs = ALIGN_CELL{i};

    ref_seq = Ref.Sequence;

    ref_prof = seqprofile(ref_seq, 'alphabet', 'aa');
    seqs_prof = seqprofile(aligned_seqs, 'alphabet', 'aa');

    [mp, H1, H2] = profalign(ref_prof, seqs_prof);

    merged_seqs = char(zeros(size(aligned_seqs,1)+1, size(mp,2)));
    merged_seqs(2:end, H2) = aligned_seqs;
    merged_seqs(1, H1) = ref_seq;

    entropy_vals = CalculateEntropy(merged_seqs);

    %only pull out the values that are in the reference positions
    ref_entropy = entropy_vals(H1);

    OUT_DATA{i} = ref_entropy;
end