相关论文: Genetic Sequence Matching Using D4M Big Data Appro…
The decreasing costs and increasing speed and accuracy of DNA sample collection, preparation, and sequencing has rapidly produced an enormous volume of genetic data. However, fast and accurate analysis of the samples remains a bottleneck.…
The ability to collect and analyze large amounts of data is a growing problem within the scientific community. The growing gap between data and users calls for innovative tools that address the challenges faced by big data volume, velocity…
Genome sequence analysis plays a pivotal role in enabling many medical and scientific advancements in personalized medicine, outbreak tracing, and forensics. However, the analysis of genome sequencing data is currently bottlenecked by 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…
Analysis of DNA samples is an important step in forensics, and the speed of analysis can impact investigations. Comparison of DNA sequences is based on the analysis of short tandem repeats (STRs), which are short DNA sequences of 2-5 base…
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…
DNA pattern matching is essential for many widely used bioinformatics applications. Disease diagnosis is one of these applications, since analyzing changes in DNA sequences can increase our understanding of possible genetic diseases. The…
The Dynamic Distributed Dimensional Data Model (D4M) library implements associative arrays in a variety of languages (Python, Julia, and Matlab/Octave) and provides a lightweight in-memory database implementation of hypersparse arrays that…
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…
Detecting anomalous behavior in network traffic is a major challenge due to the volume and velocity of network traffic. For example, a 10 Gigabit Ethernet connection can generate over 50 MB/s of packet headers. For global network providers,…
Analyzing large scale networks requires high performance streaming updates of graph representations of these data. Associative arrays are mathematical objects combining properties of spreadsheets, databases, matrices, and graphs, and are…
The D4M tool was developed to address many of today's data needs. This tool is used by hundreds of researchers to perform complex analytics on unstructured data. Over the past few years, the D4M toolbox has evolved to support connectivity…
Genome sequences contain hundreds of millions of DNA base pairs. Finding the degree of similarity between two genomes requires executing a compute-intensive dynamic programming algorithm, such as Smith-Waterman. Traditional von Neumann…
The Apache Accumulo database is an open source relaxed consistency database that is widely used for government applications. Accumulo is designed to deliver high performance on unstructured data such as graphs of network data. This paper…
In the post-genomic era, large-scale personal DNA sequences are produced and collected for genetic medical diagnoses and new drug discovery, which, however, simultaneously poses serious challenges to the protection of personal genomic…
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…
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…
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…
Protein retrieval, which targets the deconstruction of the relationship between sequences, structures and functions, empowers the advancing of biology. Basic Local Alignment Search Tool (BLAST), a sequence-similarity-based algorithm, has…
Genome sequence analysis has enabled significant advancements in medical and scientific areas such as personalized medicine, outbreak tracing, and the understanding of evolution. Unfortunately, it is currently bottlenecked by the…