Fast sequencing and analysis of (microorganism, plant or human) genomes will open up new vistas in fields like personalised medication, food yield and epigenetic research. Current state-of-the-art DNA pattern matching techniques use heuristic algorithms on computing clusters of CPUs, GPUs and FPGAs. With genomic data set to eclipse social and astronomical big data streams within a decade, the alternate computing paradigm of quantum computation is explored to accelerate genome-sequence reconstruction. The inherent parallelism of quantum superposition of states is harnessed to design a quantum kernel for accelerating the search process. The project explores the merger of these two domains and identifies ways to fit these together to design a genome-sequence analysis pipeline with quantum algorithmic speedup. The design of a genome-sequence analysis pipeline with a quantum kernel is tested with a proof-of-concept demonstration using a quantum simulator.
Fast sequencing and analysis of (microorganism, plant or human) genomes will open up new vistas in fields like personalised medication, food yield and epigenetic research. Current state-of-the-art DNA pattern matching techniques use heuristic algorithms on computing clusters of CPUs, GPUs and FPGAs. With genomic data set to eclipse social and astronomical big data streams within a decade, the alternate computing paradigm of quantum computation is explored to accelerate genome-sequence reconstruction. The inherent parallelism of quantum superposition of states is harnessed to design a quantum kernel for accelerating the search process. The project explores the merger of these two domains and identifies ways to fit these together to design a genome-sequence analysis pipeline with quantum algorithmic speedup. The design of a genome-sequence analysis pipeline with a quantum kernel is tested with a proof-of-concept demonstration using a quantum simulator.
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.
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.
This paper explores the potential of quantum algorithms to revolutionize bioinformatics, particularly in genomic analysis, protein structure prediction, and drug discovery. The core concept centers on leveraging the inherent information richness within biological datasets – specifically, DNA sequences and protein structures – to create novel quantum computational approaches. We propose a new algorithmic framework based on constructing quantum circuits directly from biological data structures, aiming to significantly accelerate computationally intensive tasks. The study emphasizes the transformative impact of this approach, focusing on the unique advantages conferred by biological information within the quantum realm. This research addresses the limitations of existing quantum computing approaches by integrating biological data into the core algorithm design.
Sequence matching in genomics can be approached by quantum computing through Grover’s algorithm offering a quadratic speed-up versus the fastest classical algorithms. Previous research using quantum computing focused on long DNA sequences, but application to complex RNA secondary structures with hairpin, bulge, ring, and stem forms has not been possible. This paper developed new formulations for RNA structures using quantum pattern recognition and quantum Hamming distance on Grover’s framework by extracting linear regions from the complex forms. To best leverage the quantum speedup, methods are developed to create long sequences by concatenating different linearized parts of the complex RNA structures. The mechanism is simulated on IBM’s Qiskit quantum simulator using RNA examples from GenBank and mirBase. Comparisons of the iteration complexity indeed shows the potential for quadratic speedups from quantum computing versus classical. Simulation results also show that search accuracy is very good when using the quantum pattern recognition method.
This research explores how quantum computing could revolutionize genomics, with a focus on how it could speed up DNA analysis and advance uses of artificial intelligence (AI) in genomics. This study’s primary objective is to investigate recent review articles and existing research results in order to demonstrate the tremendous effects that quantum computing may have on genomics.DNA analysis is expected to undergo a radical change as a result of quantum computing, which promises to revolutionize the field by substantially reducing processing times and resource needs. Additionally, it opens up fresh possibilities for improving AI methods used with genomics data. Quantum computing ushers in a paradigm shift in genomics research, enabling AI-driven drug discovery and customized medicine in addition to accelerating DNA sequencing and assembly.By addressing the significant difficulties brought on by the rapid expansion of genetic data and the requirement for more effective and scalable computational approaches, this publication emphasizes the significance of this study. The integration of quantum computing with genomics also raises ethical and security concerns, underscoring the significance of responsible research and use in this transformative era.In conclusion, this article highlights the potential of quantum computing to change genomics, delivering faster and more precise ways of analysis that will unquestionably have significant repercussions for healthcare, biotechnology, and scientific research. It emphasizes how important it is to keep up with the most recent advancements in this quickly changing area.
The exponential growth of genomic data has transformed evolutionary biology, enabling large-scale analysis of genetic variation, phylogenetic relationships, and adaptive mechanisms across species. However, classical computational approaches increasingly struggle with the combinatorial complexity, high dimensionality, and nonlinear interactions inherent in genomic datasets. This study explores how quantum-enhanced data analysis can augment evolutionary biology by enabling more efficient modeling of genomic variation and species adaptation. By leveraging quantum computing principles such as superposition, entanglement, and quantum parallelism, quantum algorithms offer the potential to accelerate sequence alignment, genotype–phenotype mapping, evolutionary optimization, and adaptive landscape exploration. Through qualitative synthesis of research in quantum computing, computational genomics, and evolutionary theory, this paper examines how quantum-enhanced frameworks can improve the detection of adaptive patterns, epistatic interactions, and evolutionary constraints. The analysis highlights potential applications in phylogenomic reconstruction, population genetics, and predictive modeling of species responses to environmental pressures. While acknowledging current technological limitations, the study argues that quantum-enhanced genomic analysis represents a promising pathway toward more scalable, precise, and predictive evolutionary models. Ultimately, this work positions quantum computing as a transformative tool for advancing our understanding of biological evolution and species resilience in rapidly changing ecosystems.