QiskitSummerJam-LocalSequenceAlignment
Our goal is to implement the Quantum Pattern Recognition (QPR) algorithm described in the paper Quantum Pattern Recognition for Local Sequence Alignment by Konstantinos Prousalis and Nikos Konofaos.
Approach
- Generate a substitution matrix of matches and non-matches using the classical Smith-Waterman algorithm.
- Transform the matrix H such that the diagonals become horizontal or vertical lines (Encode the array such that is can become the input to the quantum algorithm).
- Apply BB (Black Box, binomial classifier).
- Apply QFT.
- Measure and execute.
- Classically apply pattern localization to verify the result (dot matrix algorithm).
Dependencies
Built with the most recent versions of Qiskit and numpy (as of June 30, 2020).