Accelerating Biological Sequence Alignment Algorithm on GPU with CUDA

2011 ◽  
Author(s):  
Fang Zheng ◽  
Xianbin Xu ◽  
Yuanhua Yang ◽  
Shuibing He ◽  
Yuping Zhang
Keyword(s):  
Sequence Alignment ◽  
Alignment Algorithm ◽  
Biological Sequence ◽  
Sequence Alignment Algorithm

scholarly journals Research on Components Assembly Platform of Biological Sequences Alignment Algorithm

2021 ◽  
Vol 11 ◽  
Author(s):  
Haihe Shi ◽  
Gang Wu ◽  
Xuchu Zhang ◽  
Jun Wang ◽  
Haipeng Shi ◽  
...  
Keyword(s):  
Sequence Alignment ◽  
Alignment Algorithm ◽  
Biological Sequence ◽  
Sequence Alignment Algorithm ◽  
Alignment Algorithms ◽  
Abstract Level ◽  
Assembly Technology ◽  
Component Assembly ◽  
Efficiency And Reliability ◽  
Visual Interface

After years of development, the complexity of the biological sequence alignment algorithm is gradually increasing, and the lack of high abstract level domain research leads to the complexity of its algorithm development and improvement. By applying the idea of software components to the design and development of algorithms, the development efficiency and reliability of biological sequence alignment algorithms can be effectively improved. The component assembly platform applies related assembly technology, which simplifies the operation difficulty of component assembly and facilitates the maintenance and optimization of the algorithm. At the same time, a friendly visual interface is used to intuitively complete the assembly of algorithm components, and an executable sequence alignment algorithm program is obtained, which can directly carry out alignment computing.

scholarly journals Hardware Accelerated Sequence Alignment with Traceback

2009 ◽  
Vol 2009 ◽  
pp. 1-10 ◽  
Author(s):  
Scott Lloyd ◽  
Quinn O. Snell
Keyword(s):  
Sequence Alignment ◽  
Biomedical Applications ◽  
Sequence Length ◽  
Alignment Algorithm ◽  
Performance Gain ◽  
Biological Sequence ◽  
Timely Manner ◽  
Desktop Computer ◽  
Processing Elements ◽  
Sequence Alignment Algorithm

Biological sequence alignment is an essential tool used in molecular biology and biomedical applications. The growing volume of genetic data and the complexity of sequence alignment present a challenge in obtaining alignment results in a timely manner. Known methods to accelerate alignment on reconfigurable hardware only address sequence comparison, limit the sequence length, or exhibit memory and I/O bottlenecks. A space-efficient, global sequence alignment algorithm and architecture is presented that accelerates the forward scan and traceback in hardware without memory and I/O limitations. With 256 processing elements in FPGA technology, a performance gain over 300 times that of a desktop computer is demonstrated on sequence lengths of 16000. For greater performance, the architecture is scalable to more processing elements.

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