Related papers: A new DNA alignment method based on inverted index

Current research on DNA storage usually focuses on the improvement of storage density by developing effective encoding and decoding schemes while lacking the consideration on the uncertainty in ultra-long-term data storage and retention.…

DNA is a promising storage medium, but its stability and occurrence of Indel errors pose a significant challenge. The relative occurrence of Guanine(G) and Cytosine(C) in DNA is crucial for its longevity, and reverse complementary base…

This paper aims to present a new re-configuration sequencing method for difference of read lengths that may take place as input data in which is crucial drawbacks lay impact on DNA sequencing methods.

With current hardware and software, a standard computer can now hold in RAM an index for approximate pattern matching on about half a dozen human genomes. Sequencing technologies have improved so quickly, however, that scientists will soon…

We consider a novel approach of measuring the homology of DNA sequences based of the variety of optimal alignments in the longest common subsequence sense. The proposed approach is compared with BLAST in measuring the homology of four…

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…

Despite the constant evolution of similarity searching research, it continues to face the same challenges stemming from the complexity of the data, such as the curse of dimensionality and computationally expensive distance functions.…

Deoxyribonucleic acid (DNA) has shown great promise in enabling computational applications, most notably in the fields of DNA digital data storage and DNA computing. Information is encoded as DNA strands, which will naturally bind in…

The paper describes an algorithm to compute a consensus sequence from a set of DNA sequences of approximatively identical length generated by 3rd sequencing generation technologies. Its purpose targets DNA storage and is guided by specific…

The double digest problem is a common NP-hard approach to constructing physical maps of DNA sequences. This paper presents a new approach called the enhanced double digest problem. Although this new problem is also NP-hard, it can be solved…

The convolutional neural network (CNN) features can give a good description of image content, which usually represent images with unique global vectors. Although they are compact compared to local descriptors, they still cannot efficiently…

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…

Network alignment, in general, seeks to discover the hidden underlying correspondence between nodes across two (or more) networks when given their network structure. However, most existing network alignment methods have added assumptions of…

Several processes in the cell, such as gene regulation, start when key proteins recognise and bind to short DNA sequences. However, as these sequences can be hundreds of million times shorter than the genome, they are hard to find by simple…

In this research endeavor, some Sequence Alignment Algorithms are detailed that are useful for finding or comparing 1 dimensional (1-D), 2 dimensional (2-D), 3 dimensional (3-D) sequences in or against a parent or mother database which is 1…

Composite DNA is a recent method to increase the base alphabet size in DNA-based data storage.This paper models synthesizing and sequencing of composite DNA and introduces coding techniques to correct substitutions, losses of entire…

In DNA computing, it is impossible to decide whether a specific hybridization among complex DNA molecules is effective or not within acceptable time. In order to address this common problem, we introduce a new method based on the machine…

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…

Genomics is changing our understanding of humans, evolution, diseases, and medicines to name but a few. As sequencing technology is developed collecting DNA sequences takes less time thereby generating more genetic data every day. Today the…

Currently, third-generation sequencing techniques, which allow to obtain much longer DNA reads compared to the next-generation sequencing technologies, are becoming more and more popular. There are many possibilities to combine data from…