Three seed sequences were chosen to reflect different protein structure and different length of sequence so as to remove as far as bias in the test set. The Program RepeatMasker was used to ensure that the seed sequences were free from interspersed repeats and low-complexity regions. The Evolve program was used to generate 10 new sequences at a specific PAM distance from the seed sequences.
All programs run with default parameters.
For each database search , the top hit was labeled as correct. The coverage of the database searches was defined as the percentage of correct top hit out of all the searches carried out.