function pos = sym2pos(seq)

%SYM2POS  Converts amino acid symbols to integer indices
%  POS = sym2pos(SEQ) converts a sequence seq consisting of amino 
%  acid symbols into numerical indices corresponding to each
%  symbol, according to the standard amino acid ordering 
%  'ARNDCQEGHILKMFPSTWYV'.  This is useful if you want to 
%  efficiently access entries in a scoring matrix.  
%
%  0 corresponds to a gap ('-'), and -1 corresponds to any other
%  unrecognized  character.
%
%  See also SYM2POS

% The standard order of amino acids
symbols = 'ARNDCQEGHILKMFPSTWYV';

% Retrieve the position of each symbol
N = length(seq);
pos = zeros(1, N);
for i=1:N
  ind = findstr(symbols, seq(i));
  if (isempty(ind))
    if (seq(i) == '-')
      ind = 0;
    else
      ind = -1;
    end
  end
  pos(i) = ind;
end