Related papers: A Linear Time Quantum Algorithm for Pairwise Seque…
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…
DNA sequence alignment is important today as it is usually the first step in finding gene mutation, evolutionary similarities, protein structure, drug development and cancer treatment. Covid-19 is one recent example. There are many…
Quantum search algorithms are considered in the context of protein sequence comparison in biocomputing. 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…
We propose a quantum algorithm for closest pattern matching which allows us to search for as many distinct patterns as we wish in a given string (database), requiring a query function per symbol of the pattern alphabet. This represents a…
This paper describes a new alignment algorithm for sequences that can be used for determination of deletions and substitutions. It provides several solutions out of which the best one can be chosen on the basis of minimization of gaps or…
Reference-guided DNA sequencing and alignment is an important process in computational molecular biology. The amount of DNA data grows very fast, and many new genomes are waiting to be sequenced while millions of private genomes need to be…
Various methods have been developed to analyze the association between organisms and their genomic sequences. Among them, sequence alignment is the most frequently used for comparative analysis of biological genomes. However, the…
In genomics, pattern matching against a sequence of nucleotides plays a pivotal role for DNA sequence alignment and comparing genomes. This helps tackling some diseases, such as cancer in humans. The complexity of searching biological…
We present a quantum algorithm for solving perfect mazes by casting the pathfinding task as a structured search problem. Building on Grover's amplitude amplification, the algorithm encodes all candidate paths in superposition and evaluates…
This paper presents a new approach to statistical similarity assessment based on sequence alignment. The algorithm performs mutual matching of two random sequences by successively searching for common elements and by applying sequence…
Protein similarity searches are a routine job for molecular biologists where a query sequence of amino acids needs to be compared and ranked against an ever-growing database of proteins. All available algorithms in this field can be grouped…
Affordable, high-quality whole-genome assemblies have made it possible to construct rich pangenomes that capture haplotype diversity across many species. As these datasets grow, they motivate the development of specialized techniques…
In this paper, we implement Ant Colony Optimization (ACO) for sequence alignment. ACO is a meta-heuristic recently developed for nearest neighbor approximations in large, NP-hard search spaces. Here we use a genetic algorithm approach to…
Genetic information is encoded in a linear sequence of nucleotides, represented by letters ranging from thousands to billions. Mutations refer to changes in the DNA or RNA nucleotide sequence. Thus, mutation detection is vital in all areas…
Quantum algorithm, as compared to classical algorithm, plays a notable role in solving linear systems of equations with an exponential speedup. Here, we demonstrate a method for solving a particular system of equations by using the concept…
Quantum computation, in particular Grover's algorithm, has aroused a great deal of interest since it allows for a quadratic speedup to be obtained in search procedures. Classical search procedures for an $N$ element database require at most…
Given two sets A and B and two oracles O(A) and O(B) that can identify the elements of these sets respectively, the goal is to find an element common to both sets using minimum number of oracle queries. Each application of either O(A) or…
Grover's search algorithm is the optimal quantum algorithm that can search an unstructured database quadratically faster than any known classical algorithm. The role of entanglement and correlations in the search algorithm have been studied…
In this paper, we study Grover's search algorithm focusing on continuous-time quantum walk on graphs. We propose an alternative optimization approach to Grover's algorithm on graphs that can be summarized as follows: instead of finding…
We propose a modified MSA algorithm on quantum annealers with applications in areas of bioinformatics and genetic sequencing. To understand the human genome, researchers compare extensive sets of these genetic sequences -- or their protein…