Fast quantum search algorithms in protein sequence comparisons: quantum bioinformatics.

Abstract

Quantum search algorithms are considered in the context of protein sequence comparison in bioinformatics. Given a sample protein sequence of length m (i.e., m residues), the problem considered is to find an optimal match in a large database containing N residues. Initially, Grover's quantum search algorithm is applied to a simple illustrative case-namely, where the database forms a complete set of states over the 2(m) basis states of a m qubit register, and thus is known to contain the exact sequence of interest. This example demonstrates explicitly the typical O(square root of [N]) speedup on the classical O(N) requirements. An algorithm is then presented for the (more realistic) case where..