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Genomic signature using FCGR

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from Genomic signature using FCGR by Jesús P. Mena-Chalco
Genomic signature using Chaos game representation of frequencies.

calculateFrecuencies(sequence, word)
function freq = calculateFrecuencies(sequence, word)
% Funcion que calcula la frecuencia de 'word' en 'sequence'
% (frecuencia que considera agrupamientos sobrelapados/sobrepuestos)

    n = length(sequence);
    k = length(word);
    possibilities = n-k+1;
    freq = 0;
    
    for i=1:possibilities
        cont = 0;
        
        % contamos las igualdades para cada letra de 'word'
        for j=1:k
            if sequence(i+j-1)==word(j)
                cont = cont+1;
            else
                break; % si una letra es diferente, no es necesaria la comparacion con otras letras de la misma palabra.
            end;
        end;
        
        % Si coincide 'word' al agrupamiento entonces sumamos 1
        if (cont==k)
            freq = freq+1;
        end;
    end;
    
    freq = freq/possibilities;

end

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