The sequences were taken from the CATH database v.3.0.0 (Pearl, et al., 2005). The entries of the CATH95 (>95% identity)selection were downloaded from the ftp://ftp.biochem.ucl.ac.uk/pub/cathdata/v3.0.0/. site. The 1648 non-contiguous domains were discarded and 11373 were retained. The sequences were stored in concatenated FASTA format.

The 3D structures were taken from the CATH database v. 3.0.0(Pearl, et al., 2005). The entries of the CATH95 (>95% identity)selection were downloaded from the http://cathwww.biochem.ucl.ac.uk/staticdata/v3_0_0/dompdb/ site. The 1648 non-contiguous domains were discarded and 11 373 were retained. The structures were deposited as compressed archive.

An all against all comparison was carried out using BLAST (Altschul, et al., 1990) version 2.2.13 downloaded from http://www.ncbi.nlm.nih.gov/BLAST/download.shtml The BLOSUM62 matrix was used with a gap opening penalty of 11 and a gap extension penalty of 1 (default parameters). The results were stored in a compressed, tab-delimited ASCII file.

An all against all comparison was carried out using the Smith-Waterman algorithm (Smith and Waterman, 1981) as implemented in the water program of EMBOSS (Rice, et al., 2000). The program was downloaded from ftp://ftp.bioinformatics.org/pub/biobrew/. The BLOSUM62 matrix was used with a gap opening penalty of 10 and a gap extension penalty of 0.5 (default parameters). The results were stored in a compressed, tab-delimited ASCII file.

An all against all comparision was carried out using the Needleman-Wunsch algorithm (Needleman and Wunsch, 1970) as implemented in the needle program of EMBOSS (Rice, et al., 2000). The program was downloaded from ftp://ftp.bioinformatics.org/pub/biobrew/. The BLOSUM62 matrix was used with a gap opening penalty of 10 and a gap extension penalty of 0.5 (default). The results were stored in a compressed, tab-delimited ASCII file.

The Local Alignment Kernel program version 0.3 of Saigo and associates (Saigo, et al., 2004) was downloaded from http://cg.ensmp.fr/~vert/. The following run parameters were used: Default comparison matrix found in the parameters.h file. Gap opening penalty = 11 (default), Gap extension penalty = 1 (default), Scaling parameter = 0.5.

An all against all comparison was carried out using the PRIDE algorithm (Gaspari, et al., 2005). The program was provided by Z. Gaspari.

Nearest neighbour (1NN) classification is a technique whereby a query sequence is assigned to the a priori known class of the database entry that was found most similar to it in terms of a distance/similarity measure (for an introduction see Duda, et al., 2001).

The evaluation of classification performance was carried out by the standard receiver operator characteristic (ROC) analysis (for an introduction see (Duda, et al., 2000)). This method is designed to test the ranking ability of a given classifier based on a real-valued ranking parameter. In the case of nearest neighbour classification, the ranking parameter was a similarity/distance parameter calculated between an object and the nearest member of the positive training set (outlier detection). Briefly, the analysis is carried out by plotting sensitivity vs 1-specificity at various threshold values, then the resulting curve is integrated to give an “area under curve” or AUC value. These values are determined for each classification experiment. For a perfect ranking, AUC=1.0, for random ranking AUC=0.5 (Egan, 1975).