What's Behind Blast

The BLAST search engine was published and released in 1990. It is a heuristic that uses the idea of a neighborhood to find seed matches that are then extended. This approach came from work that this author was doing to lever these ideas to arrive at a deterministic algorithm with a characterized and superior time complexity. The resulting O(enlogn) expected-time algorithm for finding all e-matches to a string of length p in a text of length n was completed in 1991. The function pow( ) is 0 for = 0 and concave increasing, so the algorithm is truly sublinear in that its running time is O(n) for c < 1 for sufficiently small. This paper reviews the history and the unfolding of the basic concepts, and it attempts to intuitively describe the deeper result whose time-complexity, to this authors knowledge, has yet to be improved upon.