QiBAM
Approximate Sub-String Index Search on Quantum Accelerators Applied to DNA Read Alignment
Aritra Sarkar (QBee.eu, TU Delft - Computer Engineering)
Zaid Al-Ars (TU Delft - Computer Engineering)
Carmen G. Almudever (QCD/Sebastiano Lab)
Koen L.M. Bertels (QBee.eu, Katholieke Universiteit Leuven)
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Abstract
With small-scale quantum processors transitioning from experimental physics labs to industrial products, these processors in a few years are expected to scale up and be more robust for efficiently computing important algorithms in various fields. In this paper, we propose a quantum algorithm to address the challenging field of data processing for genome sequence reconstruction. This research describes an architecture-aware implementation of a quantum algorithm for sub-sequence alignment. A new algorithm named QiBAM (quantum indexed bidirectional associative memory) is proposed, which uses approximate pattern-matching based on Hamming distances. QiBAM extends the Grover’s search algorithm in two ways, allowing: (1) approximate matches needed for read errors in genomics, and (2) a distributed search for multiple solutions over the quantum encoding of DNA sequences. This approach gives a quadratic speedup over the classical algorithm. A full implementation of the algorithm is provided and verified using the OpenQL compiler and QX Simulator framework. Our implementation represents a first exploration towards a full-stack quantum accelerated genome sequencing pipeline design.
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