SSDB: Sequence Similarity Database in KEGG

Availability of a large number of complete genomes enables us to compare several genomes and to search common and different features between genomes in terms of protein sequence similarities, which we call comparative genomics. It produces information about proteins useful for the assignment of the function to genes and for the research on the evolution of the genome. The large number of genes accumulated in the databases of complete genomes, however, has become a bottleneck, because the computation of the sequence similarity of all pairs of proteins is time consuming even if we use a supercomputer. Therefore precomputed sequence similarities of completely sequenced organisms are indispensable for comparative genomics. SSDB (Sequence Similarity Database) is a new addition to the KEGG suite of databases [3] and contains the information about amino acid sequence similarities among all protein-coding genes in the complete genomes, together with the information about best hits and bidirectional best hits (best-best hits). The relation of gene x in genome A and gene y in genome B is called bidirectional best hits, when x is the best hit of query y against all genes in A and vice versa, and it is often used as an operational definition of ortholog. We report here the system design and simple search capabilities of SSDB.