Other Uses of the Blocks Database

The automated construction and extensive data in the Blocks database make it suitable for uses other than protein classification. The local alignments of sequence segments provided data for the BLOSUM series of amino acid substitution matrices. These matrices performed very well in sequence database searches. The Blocks database was also used to test and compare different methods for weighting sequences to reduce redundancy.
Many blocks are made up of sequence segments with known functions such as ligand binding regions, catalytic domains or trans-membranal domains. This can be a resource for research on specific domains. For example, when studying protein-nucleotide binding sites one can search for block families annotated as having such sites or for blocks containing the known signature of the sites. The blocks found can help refine the signature and even reveal unannotated sites.