scholarly journals High Performance Systolic Array Core Architecture Design for DNA Sequencer

2018 ◽  
Vol 150 ◽  
pp. 06009 ◽  
Author(s):  
Dayana Saiful Nurdin ◽  
Mohd. Nazrin Md. Isa ◽  
Rizalafande Che Ismail ◽  
Muhammad Imran Ahmad
Keyword(s):  
Systolic Array ◽  
Dna Sequences ◽  
High Performance ◽  
Computation Time ◽  
Local Alignment ◽  
Architecture Design ◽  
Alignment Algorithm ◽  
The Core ◽  
Field Programmable ◽  
Dna Sequencer

This paper presents a high performance systolic array (SA) core architecture design for Deoxyribonucleic Acid (DNA) sequencer. The core implements the affine gap penalty score Smith-Waterman (SW) algorithm. This time-consuming local alignment algorithm guarantees optimal alignment between DNA sequences, but it requires quadratic computation time when performed on standard desktop computers. The use of linear SA decreases the time complexity from quadratic to linear. In addition, with the exponential growth of DNA databases, the SA architecture is used to overcome the timing issue. In this work, the SW algorithm has been captured using Verilog Hardware Description Language (HDL) and simulated using Xilinx ISIM simulator. The proposed design has been implemented in Xilinx Virtex -6 Field Programmable Gate Array (FPGA) and improved in the core area by 90% reduction.

scholarly journals A Systolic Array-Based FPGA Parallel Architecture for the BLAST Algorithm

2012 ◽  
Vol 2012 ◽  
pp. 1-11 ◽  
Author(s):  
Xinyu Guo ◽  
Hong Wang ◽  
Vijay Devabhaktuni
Keyword(s):  
Systolic Array ◽  
Clock Cycle ◽  
Parallel Architecture ◽  
Second Step ◽  
Local Alignment ◽  
Alignment Algorithm ◽  
Biological Sequence ◽  
Sequence Alignment Algorithm ◽  
Field Programmable ◽  
Search Tool

A design of systolic array-based Field Programmable Gate Array (FPGA) parallel architecture for Basic Local Alignment Search Tool (BLAST) Algorithm is proposed. BLAST is a heuristic biological sequence alignment algorithm which has been used by bioinformatics experts. In contrast to other designs that detect at most one hit in one-clock-cycle, our design applies a Multiple Hits Detection Module which is a pipelining systolic array to search multiple hits in a single-clock-cycle. Further, we designed a Hits Combination Block which combines overlapping hits from systolic array into one hit. These implementations completed the first and second step of BLAST architecture and achieved significant speedup comparing with previously published architectures.

scholarly journals Enabling Packet Classification with Low Update Latency for SDN Switch on FPGA

2020 ◽  
Vol 12 (8) ◽  
pp. 3068 ◽  
Author(s):  
Chenglong Li ◽  
Tao Li ◽  
Junnan Li ◽  
Zilin Shi ◽  
Baosheng Wang
Keyword(s):  
Real Time ◽  
Field Programmable Gate Array ◽  
High Performance ◽  
Recursive Algorithm ◽  
Packet Classification ◽  
Experimental Results ◽  
The Core ◽  
Core Function ◽  
Field Programmable ◽  
Bit Vector

Field Programmable Gate Array (FPGA) is widely used in real-time network processing such as Software-Defined Networking (SDN) switch due to high performance and programmability. Bit-Vector (BV)-based approaches can implement high-performance multi-field packet classification, on FPGA, which is the core function of the SDN switch. However, the SDN switch requires not only high performance but also low update latency to avoid controller failure. Unfortunately, the update latency of BV-based approaches is inversely proportional to the number of rules, which means can hardly support the SDN switch effectively. It is reasonable to split the ruleset into sub-rulesets that can be performed in parallel, thereby reducing update latency. We thus present SplitBV for the efficient update by using several distinguishable exact-bits to split the ruleset. SplitBV consists of a constrained recursive algorithm for selecting the bit positions that can minimize the latency and a hybrid lookup pipeline. It can achieve a significant reduction in update latency with negligible memory growth and comparable high performance. We implement SplitBV and evaluate its performance by simulation and FPGA prototype. Experimental results show that our approach can reduce 73% and 36% update latency on average for synthetic 5-tuple rules and OpenFlow rules respectively.

scholarly journals Acceleration of Nucleotide Semi-Global Alignment with Adaptive Banded Dynamic Programming

2017 ◽  
Author(s):  
Hajime Suzuki ◽  
Masahiro Kasahara
Keyword(s):  
Dynamic Programming ◽  
Single Molecule ◽  
Computation Time ◽  
Error Rates ◽  
Nucleotide Sequences ◽  
Sequencing Error ◽  
Local Alignment ◽  
Global Alignment ◽  
Alignment Algorithm ◽  
Short Read

AbstractMotivationPairwise alignment of nucleotide sequences has previously been carried out using the seed- and-extend strategy, where we enumerate seeds (shared patterns) between sequences and then extend the seeds by Smith-Waterman-like semi-global dynamic programming to obtain full pairwise alignments. With the advent of massively parallel short read sequencers, algorithms and data structures for efficiently finding seeds have been extensively explored. However, recent advances in single-molecule sequencing technologies have enabled us to obtain millions of reads, each of which is orders of magnitude longer than those output by the short-read sequencers, demanding a faster algorithm for the extension step that accounts for most of the computation time required for pairwise local alignment. Our goal is to design a faster extension algorithm suitable for single-molecule sequencers with high sequencing error rates (e.g., 10-15%) and with more frequent insertions and deletions than substitutions.ResultsWe propose an adaptive banded dynamic programming algorithm for calculating pairwise semi-global alignment of nucleotide sequences that allows a relatively high insertion or deletion rate while keeping band width relatively low (e.g., 32 or 64 cells) regardless of sequence lengths. Our new algorithm eliminated mutual dependences between elements in a vector, allowing an efficient Single-Instruction-Multiple-Data parallelization. We experimentally demonstrate that our algorithm runs approximately 5× faster than the extension alignment algorithm in NCBI BLAST+ while retaining similar sensitivity (recall).We also show that our extension algorithm is more sensitive than the extension alignment routine in DALIGNER, while the computation time is comparable.AvailabilityThe implementation of the algorithm and the benchmarking scripts are available at https://github.com/ocxtal/[email protected]

scholarly journals EOBAA: Enhanced Ontology Based Alignment Algorithm for Mining Frequent Patterns

2018 ◽  
Vol 7 (3.12) ◽  
pp. 157
Author(s):  
D Srinivasa Rao ◽  
V Sucharitha ◽  
K V.V Satyanarayana
Keyword(s):  
Real Time ◽  
High Performance ◽  
Computation Time ◽  
Search Space ◽  
Search Tree ◽  
Frequent Itemsets ◽  
Alignment Algorithm ◽  
Frequent Patterns ◽  
Pruning Strategy ◽  
Real Time Applications

Mining frequent patterns are most widely used in many applications such as supermarkets, diagnostics, and other real-time applications. Performance of the algorithm is calculated based on the computation of the algorithm. It is very tedious to compute the frequent patterns in mining. Many algorithms and techniques are implemented and studied to generate the high-performance algorithms such as Prepost+ which employees the N-list to represent itemsets and directly discovers frequent itemsets using a set-enumeration search tree. But due to its pruning strategy, it is known that the computation time is more for processing the search space. It enumerates all item sets from datasets by the principle of exhaustion and they don’t sort them based on utility, but only a statistical proof of most recurring itemset. In this paper, the proposed Enhanced Ontologies based Alignment Algorithm (EOBAA) to identify, extract, sort out the HUI's from FI's. To improve the similarity measure the proposed system adopted Cosine similarity. The experiments conducted on 1 real datasets and show the performance of the EOBAA based on the computation time and accuracy of the proposed EOBAA.  

scholarly journals High-Performance Time Server Core for FPGA System-on-Chip

Electronics ◽  
2019 ◽  
Vol 8 (5) ◽  
pp. 528 ◽  
Author(s):  
Julian Viejo ◽  
Jorge Juan-Chico ◽  
Manuel J. Bellido ◽  
Paulino Ruiz-de-Clavijo ◽  
David Guerrero ◽  
...  
Keyword(s):  
High Performance ◽  
System On Chip ◽  
The Core ◽  
Performance Time ◽  
Network Time ◽  
Wide Range ◽  
Network Time Protocol ◽  
Field Programmable ◽  
And Performance ◽  
On Chip

This paper presents the complete design and implementation of a low-cost, low-footprint, network time protocol server core for field programmable gate arrays. The core uses a carefully designed modular architecture, which is fully implemented in hardware using digital circuits and systems. Most remarkable novelties introduced are a hardware-optimized timekeeping algorithm implementation, and a full-hardware protocol stack and automatic network configuration. As a result, the core is able to achieve similar accuracy and performance to typical high-performance network time protocol server equipment. The core uses a standard global positioning system receiver as time reference, has a small footprint and can easily fit in a low-range field-programmable chip, greatly scaling down from previous system-on-chip time synchronization systems. Accuracy and performance results show that the core can serve hundreds of thousands of network time clients with negligible accuracy degradation, in contrast to state-of-the-art high-performance time server equipment. Therefore, this core provides a valuable time server solution for a wide range of emerging embedded and distributed network applications such as the Internet of Things and the smart grid, at a fraction of the cost and footprint of current discrete and embedded solutions.

Denaturing High Performance Liquid Chromatography and Bioinformatics - Two Modern Tools for Extracellular Superoxide Dismutase (SOD3) Gene Promoter Analysis

2008 ◽  
Vol 59 (7) ◽  
Author(s):  
Corina Samoila ◽  
Alfa Xenia Lupea ◽  
Andrei Anghel ◽  
Marilena Motoc ◽  
Gabriela Otiman ◽  
...  
Keyword(s):  
High Performance Liquid Chromatography ◽  
Transcription Factors ◽  
Liquid Chromatography ◽  
Dna Sequences ◽  
High Performance ◽  
Zinc Finger Protein ◽  
High Capacity ◽  
Gene Promoter ◽  
Experimental Approaches ◽  
Myeloid Zinc Finger

Denaturing High Performance Liquid Chromatography (DHPLC) is a relatively new method used for screening DNA sequences, characterized by high capacity to detect mutations/polymorphisms. This study is focused on the Transgenomic WAVETM DNA Fragment Analysis (based on DHPLC separation method) of a 485 bp fragment from human EC-SOD gene promoter in order to detect single nucleotide polymorphism (SNPs) associated with atherosclerosis and risk factors of cardiovascular disease. The fragment of interest was amplified by PCR reaction and analyzed by DHPLC in 100 healthy subjects and 70 patients characterized by atheroma. No different melting profiles were detected for the analyzed DNA samples. A combination of computational methods was used to predict putative transcription factors in the fragment of interest. Several putative transcription factors binding sites from the Ets-1 oncogene family: ETS member Elk-1, polyomavirus enhancer activator-3 (PEA3), protein C-Ets-1 (Ets-1), GABP: GA binding protein (GABP), Spi-1 and Spi-B/PU.1 related transcription factors, from the Krueppel-like family: Gut-enriched Krueppel-like factor (GKLF), Erythroid Krueppel-like factor (EKLF), Basic Krueppel-like factor (BKLF), GC box and myeloid zinc finger protein MZF-1 were identified in the evolutionary conserved regions. The bioinformatics results need to be investigated further in others studies by experimental approaches.

scholarly journals The structure of ORC–Cdc6 on an origin DNA reveals the mechanism of ORC activation by the replication initiator Cdc6

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Xiang Feng ◽  
Yasunori Noguchi ◽  
Marta Barbon ◽  
Bruce Stillman ◽  
Christian Speck ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Origin Recognition Complex ◽  
Molecular Level ◽  
Dna Recognition ◽  
Winged Helix ◽  
Replicative Helicase ◽  
The Core ◽  
Α Helix ◽  
Replication Initiator ◽  
Winged Helix Domain

AbstractThe Origin Recognition Complex (ORC) binds to sites in chromosomes to specify the location of origins of DNA replication. The S. cerevisiae ORC binds to specific DNA sequences throughout the cell cycle but becomes active only when it binds to the replication initiator Cdc6. It has been unclear at the molecular level how Cdc6 activates ORC, converting it to an active recruiter of the Mcm2-7 hexamer, the core of the replicative helicase. Here we report the cryo-EM structure at 3.3 Å resolution of the yeast ORC–Cdc6 bound to an 85-bp ARS1 origin DNA. The structure reveals that Cdc6 contributes to origin DNA recognition via its winged helix domain (WHD) and its initiator-specific motif. Cdc6 binding rearranges a short α-helix in the Orc1 AAA+ domain and the Orc2 WHD, leading to the activation of the Cdc6 ATPase and the formation of the three sites for the recruitment of Mcm2-7, none of which are present in ORC alone. The results illuminate the molecular mechanism of a critical biochemical step in the licensing of eukaryotic replication origins.

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