Related papers: DNA Pattern Matching Acceleration with Analog Resi…
Recent DNA pre-alignment filter designs employ DRAM for storing the reference genome and its associated meta-data. However, DRAM incurs increasingly high energy consumption background and refresh energy as devices scale. To overcome this…
The alignment of biological sequences such as DNA, RNA, and proteins, is one of the basic tools that allow to detect evolutionary patterns, as well as functional/structural characterizations between homologous sequences in different…
Genomic data sets are growing dramatically as the cost of sequencing continues to decline and small sequencing devices become available. Enormous community databases store and share this data with the research community, but some of these…
High quality AI solutions require joint optimization of AI algorithms, such as deep neural networks (DNNs), and their hardware accelerators. To improve the overall solution quality as well as to boost the design productivity, efficient…
Pattern Matching is a computationally intensive task used in many research fields and real world applications. Due to the ever-growing volume of data to be processed, and increasing link speeds, the number of patterns to be matched has…
The search for similar genetic sequences is one of the main bioinformatics tasks. The genetic sequences data banks are growing exponentially and the searching techniques that use linear time are not capable to do the search in the required…
This paper presents a novel DNA sequences alignment method based on inverted index. Now most large scale information retrieval system are all use inverted index as the basic data structure. But its application in DNA sequence alignment is…
We present an assignment for a full Parallel Computing course. Since 2017/2018, we have proposed a different problem each academic year to illustrate various methodologies for approaching the same computational problem using different…
Recent technological advances in Next Generation Sequencing tools have led to increasing speeds of DNA sample collection, preparation, and sequencing. One instrument can produce over 600 Gb of genetic sequence data in a single run. This…
Genome sequencing has become a central focus in computational biology. A genome study typically begins with sequencing, which produces millions to billions of short DNA fragments known as reads. Read mapping aligns these reads to a…
Content addressable memory (CAM) is widely used in associative search tasks for its highly parallel pattern matching capability. To accommodate the increasingly complex and data-intensive pattern matching tasks, it is critical to keep…
Artificial synthesis of DNA molecules is an essential part of the study of biological mechanisms. The design of a synthetic DNA molecule usually involves many objectives. One of the important objectives is to eliminate short sequence…
DNA computing is an unconventional approach to computing that harnesses the parallelism and information storage capabilities of DNA molecules. It has emerged as a promising field with potential applications in solving a variety of…
Pattern matching on large graphs is the foundation for a variety of application domains. Strict latency requirements and continuously increasing graph sizes demand the usage of highly parallel in-memory graph processing engines that need to…
Upcoming many core processors are expected to employ a distributed memory architecture similar to currently available supercomputers, but parallel pattern mining algorithms amenable to the architecture are not comprehensively studied. We…
Genetic information is increasing exponentially, doubling every 18 months. Analyzing this information within a reasonable amount of time requires parallel computing resources. While considerable research has addressed DNA analysis using…
Sequence alignment is a cornerstone of bioinformatics, widely used to identify similarities between DNA, RNA, and protein sequences and studying evolutionary relationships and functional properties. The Needleman-Wunsch algorithm remains a…
DNA is a leading candidate as the next archival storage media due to its density, durability and sustainability. To read (and write) data DNA storage exploits technology that has been developed over decades to sequence naturally occurring…
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…
The Aho-Corasick algorithm is multiple patterns searching algorithm running sequentially in various applications like network intrusion detection and bioinformatics for finding several input strings within a given large input string. The…