Indexing and retrieval for genomic databases

Genomic sequence databases are widely used by molecular biologists for homology searching. Amino acid and nucleotide databases are increasing in size exponentially, and mean sequence lengths are also increasing. In searching such databases, it is desirable to use heuristics to perform computationally intensive local alignments on selected sequences and to reduce the costs of the alignments that are attempted. We present an index-based approach for both selecting sequences that display broad similarity to a query and for fast local alignment. We show experimentally that the indexed approach results in significant savings in computationally intensive local alignments and that index-based searching is as accurate as existing exhaustive search schemes.