Related papers: Iterative Learning for Reference-Guided DNA Sequen…

This paper focuses on pattern matching in the DNA sequence. It was inspired by a previously reported method that proposes encoding both pattern and sequence using prime numbers. Although fast, the method is limited to rather small pattern…

In the last decade a number of algorithms and associated software have been developed to align next generation sequencing (NGS) reads with relevant reference genomes. The accuracy of these programs may vary significantly, especially when…

DNA sequence alignment involves assigning short DNA reads to the most probable locations on an extensive reference genome. This process is crucial for various genomic analyses, including variant calling, transcriptomics, and epigenomics.…

Message-passing algorithms based on the Belief Propagation (BP) equations constitute a well-known distributed computational scheme. It is exact on tree-like graphical models and has also proven to be effective in many problems defined on…

DNA sequencing is the physical/biochemical process of identifying the location of the four bases (Adenine, Guanine, Cytosine, Thymine) in a DNA strand. As semiconductor technology revolutionized computing, modern DNA sequencing technology…

We present a framework for the design of optimal assembly algorithms for shotgun sequencing under the criterion of complete reconstruction. We derive a lower bound on the read length and the coverage depth required for reconstruction in…

In this paper, we propose a novel iterative encoding algorithm for DNA storage to satisfy both the GC balance and run-length constraints using a greedy algorithm. DNA strands with run-length more than three and the GC balance ratio far from…

Genome assembly from the high-throughput sequencing (HTS) reads is a fundamental yet challenging computational problem. An intrinsic challenge is the uncertainty caused by the widespread repetitive elements. Here we get around the…

DNA sequencing to identify genetic variants is becoming increasingly valuable in clinical settings. Assessment of variants in such sequencing data is commonly implemented through Bayesian heuristic algorithms. Machine learning has shown…

Pyrosequencing is among the emerging sequencing techniques, capable of generating upto 100,000 overlapping reads in a single run. This technique is much faster and cheaper than the existing state of the art sequencing technique such as…

De novo genome assembly, i.e., rebuilding the sequence of an unknown genome from redundant and erroneous short sequences, is a key but computationally intensive step in many genomics pipelines. The exponential growth of genomic data is…

There are currently plenty of programs available for mapping short sequences (reads) to a genome. Most of them, however, including such popular and actively developed programs as Bowtie, BWA, TopHat and many others, are based on…

A critical step of genome sequence analysis is the mapping of sequenced DNA fragments (i.e., reads) collected from an individual to a known linear reference genome sequence (i.e., sequence-to-sequence mapping). Recent works replace the…

Reducing the cost of sequencing genomes provided by next-generation sequencing technologies has greatly increased the number of genomic projects. As a result, there is a growing need for better assembly and assembly validation methods. One…

Massively parallel sequencing techniques have revolutionized biological and medical sciences by providing unprecedented insight into the genomes of humans, animals, and microbes. Modern sequencing platforms generate enormous amounts of…

Most DNA sequencing technologies are based on the shotgun paradigm: many short reads are obtained from random unknown locations in the DNA sequence. A fundamental question, studied in arXiv:1203.6233, is what read length and coverage depth…

Feature embedding methods have been proposed in literature to represent sequences as numeric vectors to be used in some bioinformatics investigations, such as family classification and protein structure prediction. Recent theoretical…

DNA sequencing is the process of determining the exact order of the nucleotide bases of an individual's genome in order to catalogue sequence variation and understand its biological implications. Whole-genome sequencing techniques produce…

This paper seeks to address the question of designing distributed algorithms for the setting of compact memory i.e. sublinear bits working memory for arbitrary connected networks. The nodes in our networks may have much lower internal…

Optimal reconstruction of a source sequence from multiple noisy traces corrupted by random insertions, deletions, and substitutions typically requires joint processing of all traces, leading to computational complexity that grows…