GPU-Based Cloud Service for Smith-Waterman Algorithm Using Frequency Distance Filtration Scheme
نویسندگان
چکیده
منابع مشابه
GPU-Based Cloud Service for Smith-Waterman Algorithm Using Frequency Distance Filtration Scheme
As the conventional means of analyzing the similarity between a query sequence and database sequences, the Smith-Waterman algorithm is feasible for a database search owing to its high sensitivity. However, this algorithm is still quite time consuming. CUDA programming can improve computations efficiently by using the computational power of massive computing hardware as graphics processing units...
متن کاملAccelerating Smith-Waterman Alignment for Protein Database Search Using Frequency Distance Filtration Scheme Based on CPU-GPU Collaborative System
The Smith-Waterman (SW) algorithm has been widely utilized for searching biological sequence databases in bioinformatics. Recently, several works have adopted the graphic card with Graphic Processing Units (GPUs) and their associated CUDA model to enhance the performance of SW computations. However, these works mainly focused on the protein database search by using the intertask parallelization...
متن کاملGPU Accelerated Smith-Waterman
We present a novel hardware implementation of the double affine Smith-Waterman (DASW) algorithm, which uses dynamic programming to compare and align genomic sequences such as DNA and proteins. We implement DASW on a commodity graphics card, taking advantage of the general purpose programmability of the graphics processing unit to leverage its cheap parallel processing power. The results demonst...
متن کاملCommunication Optimization for Multi GPU Implementation of Smith-Waterman Algorithm
GPU parallelism for real applications can achieve enormous performance gain. CPU-GPU Communication is one of the major bottlenecks that limit this performance gain. Among several libraries developed so far to optimize this communication, DyManD (Dynamically Managed Data) provides better communication optimization strategies and achieves better performance on a single GPU. SmithWaterman is a wel...
متن کاملParallel Smith-Waterman Algorithm for Gene Sequencing
Smith-Waterman Algorithm represents a highly robust and efficient parallel computing system development for biological gene sequence. The research work here gives a deep understanding and knowledge transfer about exiting approach for gene sequencing and alignment using Smith-waterman their strength and weaknesses. Smith-Waterman algorithm calculates the local alignment of two given sequences us...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: BioMed Research International
سال: 2013
ISSN: 2314-6133,2314-6141
DOI: 10.1155/2013/721738