Related papers: SeqManager: A Web-Based Tool for Efficient Sequenc…
Calculating the similarities between a pair of genomic sequences is one of the most fundamental computational steps in genomic analysis. This step -- called sequence alignment -- is the computational bottleneck because: (1) it is…
Repetitive DNA (repeats) poses significant challenges for accurate and efficient genome assembly and sequence alignment. This is particularly true for metagenomic data, where genome dynamics such as horizontal gene transfer, gene…
With the development of high throughput sequencing technology, it becomes possible to directly analyze mutation distribution in a genome-wide fashion, dissociating mutation rate measurements from the traditional underlying assumptions.…
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…
Motivation: Quality control of genomic data is an essential but complicated multi-step procedure, often requiring separate installation and expert familiarity with a combination of disparate bioinformatics tools. Results: To provide an…
We introduce a pipeline to easily generate collections of web accessible UCSC genome browsers interrelated by an alignment. Using the alignment, all annotations and the alignment itself can be efficiently viewed with reference to any genome…
Identification of functional elements of a genome often requires dividing a sequence of measurements along a genome into segments differing from adjacent segments. In many applications, the mean of the measured values at multiple genomic…
During genomics life science research, the data volume of whole genomics and life science algorithm is going bigger and bigger, which is calculated as TB, PB or EB etc. The key problem will be how to store and analyze the data with…
Online learning platforms provide diverse questions to gauge the learners' understanding of different concepts. The repository of questions has to be constantly updated to ensure a diverse pool of questions to conduct assessments for…
Sequential dense retrieval models utilize advanced sequence learning techniques to compute item and user representations, which are then used to rank relevant items for a user through inner product computation between the user and all item…
With the advent of Next-Generation (NG) sequencing, it has become possible to sequence an entire genome quickly and inexpensively. However, in some experiments one only needs to extract and assembly a portion of the sequence reads, for…
As sequencing technologies become more affordable and genomic databases expand continuously, the reuse of publicly available sequencing data emerges as a powerful strategy for studying microbial pathogens. Indeed, raw sequencing reads…
Identification of cognates across related languages is one of the primary problems in historical linguistics. Automated cognate identification is helpful for several downstream tasks including identifying sound correspondences,…
The third-generation long reads sequencing technologies, such as PacBio and Nanopore, have great advantages over second-generation Illumina sequencing in de novo assembly studies. However, due to the inherent low base accuracy,…
Single-stranded libraries generated from ancient DNA extracts have specific sequencing requirements. The short library molecules typically associated with ancient DNA templates are expected to behave differently during the annealing to the…
Modern high throughput sequencing technologies like metagenomic sequencing generate millions of sequences which have to be classified based on their taxonomic rank. Modern approaches either apply local alignment and comparison to existing…
Log-based predictive maintenance of computing centers is a main concern regarding the worldwide computing grid that supports the CERN (European Organization for Nuclear Research) physics experiments. A log, as event-oriented adhoc…
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…
Labeling of DNA molecules is a fundamental technique for DNA visualization and analysis. This process was mathematically modeled in [1], where the received sequence indicates the positions of the used labels. In this work, we develop error…
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…