Motivation: The exponential growth of publicly available genomic data has created unprecedented opportunities for sequence-based discovery. Locating specific k-mers is fundamental to diverse applications, including metagenomic classification, pathogen and cancer detection, and variant calling yet efficient identification of multiple k-mer patterns across large sequencing data and massive databases remains a significant computational challenge. Method: We implement two quantum algorithms for DNA multi-pattern string matching for k-mer detection, leveraging Grover's amplitude amplification under the idealized quantum random access memory (QRAM) framework. The first algorithm uses an enumerate-m oracle that sequentially checks a loaded text substring against all m patterns achieving O (√S) query complexity for S text positions but requiring O (m · L) work per oracle call. The second algorithm employs nested Grover search with an outer loop over text positions and an inner loop over pattern space, reducing oracle complexity to O(L) while performing O (√S · √m) in total. These asymptotic gains highlight the potential advantages that could be unlocked by future large-scale, low-noise QRAM architectures, positioning our results as a promising proof-of-concept foundation. Results: This work introduces two quantum implementations of multi-pattern string matching tailored for k-mer detection. Leveraging quantum parallelism and Grover-inspired search primitives, our methods accelerate dictionary-based pattern matching, particularly in contexts involving large sequences, such as genomic data, and extensive pattern sets. Conclusion: While implementation challenges such as QRAM overhead remain, this study demonstrates both the promise and current limitations of quantum-enhanced string matching, establishing a foundational step toward quantum readiness in bioinformatics. Availability and Implementation: To maximize accessibility and practical use, we provide our methodology at: https://github.com/Georgakopoulos-Soares-lab/quantum-multi-motif-finder.
Motivation: The exponential growth of publicly available genomic data has created unprecedented opportunities for sequence-based discovery. Locating specific k-mers is fundamental to diverse applications, including metagenomic classification, pathogen and cancer detection, and variant calling yet efficient identification of multiple k-mer patterns across large sequencing data and massive databases remains a significant computational challenge. Method: We implement two quantum algorithms for DNA multi-pattern string matching for k-mer detection, leveraging Grover's amplitude amplification under the idealized quantum random access memory (QRAM) framework. The first algorithm uses an enumerate-m oracle that sequentially checks a loaded text substring against all m patterns achieving O (√S) query complexity for S text positions but requiring O (m · L) work per oracle call. The second algorithm employs nested Grover search with an outer loop over text positions and an inner loop over pattern space, reducing oracle complexity to O(L) while performing O (√S · √m) in total. These asymptotic gains highlight the potential advantages that could be unlocked by future large-scale, low-noise QRAM architectures, positioning our results as a promising proof-of-concept foundation. Results: This work introduces two quantum implementations of multi-pattern string matching tailored for k-mer detection. Leveraging quantum parallelism and Grover-inspired search primitives, our methods accelerate dictionary-based pattern matching, particularly in contexts involving large sequences, such as genomic data, and extensive pattern sets. Conclusion: While implementation challenges such as QRAM overhead remain, this study demonstrates both the promise and current limitations of quantum-enhanced string matching, establishing a foundational step toward quantum readiness in bioinformatics. Availability and Implementation: To maximize accessibility and practical use, we provide our methodology at: https://github.com/Georgakopoulos-Soares-lab/quantum-multi-motif-finder.
Motivation: The exponential growth of publicly available genomic data has created unprecedented opportunities for sequence-based discovery. Locating specific k-mers is fundamental to diverse applications, including metagenomic classification, pathogen and cancer detection, and variant calling yet efficient identification of multiple k-mer patterns across large sequencing data and massive databases remains a significant computational challenge. Method: We implement two quantum algorithms for DNA multi pattern string matching for k-mer detection based on Grover's amplitude amplification with quantum random access memory (QRAM). The first algorithm uses an enumerate-m oracle that sequentially checks a loaded text substring against all m patterns achieving O(√S) query complexity for S text positions but requiring O(m·L) work per oracle call. The second algorithm employs nested Grover search with an outer loop over text positions and an inner loop over pattern space, reducing oracle complexity to O(L) while performing O(√S · √m) in total. Results: We present two quantum implementations of multi-pattern string matching tailored for k-mer detection. Leveraging quantum parallelism and Grover-inspired search primitives, our methods accelerate dictionary-based pattern matching, particularly in contexts involving large sequences, such as genomic data, and extensive pattern sets. Conclusions: While implementation challenges such as QRAM overhead remain, this study demonstrates both the promise and current limitations of quantum-enhanced string matching, establishing a foundational step toward quantum readiness in bioinformatics.
The exponential growth of genomic data presents significant computational challenges in the field of bioinformatics, particularly in genome sequencing. Traditional methods struggle to meet the increasing demand for speed, accuracy, and efficiency. This paper introduces a novel framework that leverages quantum computing to accelerate genome sequencing processes. The proposed framework integrates quantum algorithms, such as Grover's search and quantum Fourier transform, with classical bioinformatics techniques to optimize key tasks, including sequence alignment, variant detection, and large-scale data analysis. By exploiting the inherent parallelism and computational power of quantum systems, the framework achieves substantial reductions in processing time while maintaining high accuracy. A case study on large-scale genomic datasets demonstrates the framework's ability to outperform state-of-the-art classical approaches, particularly in handling complex and large-scale sequencing tasks. Furthermore, this research highlights the potential of quantum computing in advancing bioinformatics, paving the way for more efficient and scalable solutions to address the computational bottlenecks of modern genomics. The implications of this interdisciplinary approach extend beyond genomics, offering transformative possibilities in data-driven life sciences.
With small-scale quantum processors transitioning from experimental physics labs to industrial products, these processors allow us to efficiently compute important algorithms in various fields. In this paper, we propose a quantum algorithm to address the challenging field of big 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, that uses approximate pattern-matching based on Hamming distances. QiBAM extends the Grover's search algorithm in two ways to allow for: (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. This represents a first exploration towards a full-stack quantum accelerated genome sequencing pipeline design. The open-source implementation can be found on https://github.com/prince-ph0en1x/QAGS.
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.
Finding highly similar pairs of biological sequences is a fundamental task in bioinformatics. For alignment-free k-mer distributional similarities, the induced feature space is high-dimensional and lacks the low-dimensional geometric structure used by classical exact closest-pair algorithms. Thus, for a collection of N sequences in the pairwise-score setting, exhaustive evaluation over the binom(N,2) candidate pairs is the natural classical baseline. We present the first quantum framework targeting alignment-free closest-pair search in biological sequence collections using distributional k-mer statistics. The central technical contribution is the construction of a coherent pairwise-score estimation circuit for this similarity measure. It encodes empirical k-mer distributions as square-root amplitude states and provides a sparse prefix-tree construction for preparing these states, under which the state overlap is exactly the Bhattacharyya coefficient. Standard SWAP-test and quantum-amplitude-estimation subroutines provide a coherent bounded-precision estimator for the squared Bhattacharyya overlap. We analyze maximum finding under an explicit assumption that a fixed ε-resolved total order over all legal pairs admits an efficient clean coherent implementation. Under this assumption, the procedure returns, with probability at least 2/3, a pair whose squared Bhattacharyya score is within ε of the optimal score, using O(N) expected comparison-oracle calls. If the optimal score is separated from every strictly suboptimal score by more than ε, the returned pair is exactly optimal. Combining this comparison-order assumption with an idealized qRAM-style data-access model gives the conditional sequential gate complexity Õ(NL/ε), whereas explicit multiplexed indexed loading gives Õ(N²L/ε). We also provide a proof-of-concept Q#implementation that integrates coherent indexed loading, SWAP-test-based score estimation, finite-precision marking, and Grover-style search, providing circuit-level validation of the main computational components.
The landmark Grover algorithm for amplitude amplification serves as an essential subroutine in various types of quantum algorithms, with guaranteed quantum speedup in query complexity. However, there has been no proposal to realize the original motivating application of the algorithm, i.e., the database search or more broadly the pattern matching in a practical setting, mainly due to the technical difficulty in efficiently implementing the data loading and amplitude amplification processes. In this paper, we propose a quantum algorithm that approximately executes the entire Grover database search or pattern matching algorithm. The key idea is to use the recently proposed approximate amplitude encoding method on a shallow quantum circuit, together with the easily implementable inversion-test operation for realizing the projected quantum state having similarity to the query data, followed by the amplitude amplification operation that is independent to the target data index. We provide a thorough demonstration of the algorithm in the problem of image pattern matching.