stringkerneldemo.m

Proteins _ String Kernel

%This file compares two string kernel similarity measures. The first is a simple string kernel,
%and the second is the mismatch kernel.

%Arthur Gretton


%Input two strings

disp('NOTE: strings must contain only characters "a" through "z", since this code was designed for protein strings')

string1 = input('Type the first string:','s');
string2 = input('Type the second string:','s');
seqLength=input('Length of the subsequences being compared:')

bothStrings={string1,string2};
K_simple = simpleStringKernel(seqLength,bothStrings);
K_mismatch = mismatchStringKernel(seqLength,bothStrings);

disp('The spectrum kernel similarity score is:');
K_simple
disp('The mismatch kernel similarity score is:');
K_mismatch