In response to the comment of Hu et al., we addressed the problem on the normalization of leading eigenvalue of the L/L matrix and state that the normalized leading eigenvalue of L/L matrix depends somewhat on N (the length of the sequence)-hence when one compares L/L matrices of different N this has to be taken into account. Since the leading eigenvalues are matrix invariants frequently used in the analysis of similarities, this discussion is significative. (c) 2006 Elsevier B.V. All rights reserved.