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PIPE parameter tuning. In (a) the measured probability for two random fragments to match with a given PAM120 score (fragment score) is shown to be 10-6 for scores larger than 35. This was done using 1 M random fragment pairs of length 20. In (b) 1,000 random protein pairs of length 500 are used to show that the measured probability for two random proteins to have a maximum PIPE score larger than 10 is 10-6.
