DocumentCode :
3193322
Title :
GPU-based cloud service for multiple sequence alignments with regular expression constrains
Author :
Yu-Shiang Lin ; Chun-Yuan Lin ; Yeh-Ching Chung
Author_Institution :
Dept. of Comput. Sci., Nat. Tsing Hua Univ., Hsinchu, Taiwan
fYear :
2012
fDate :
3-6 Dec. 2012
Firstpage :
741
Lastpage :
746
Abstract :
Multiple sequence alignments with constrains has become an important problem in the computational biology. The concept of constrained sequence alignment is proposed to incorporate the biologist´s domain knowledge into sequence alignments such that the user-specified residues/segments are aligned together in the alignment results. Over the past decade, a series of constrained multiple sequence alignment tools were proposed in the literature. GPU-REMuSiC is a newest tool with the regular expression constrains and uses the graphics processing units (GPUs) with CUDA. GPU-REMuSiC can achieve 29× speedups for overall computation time by the experimental results. However, the execution environment of GPU-REMuSiC need to build, and it´s a threshold for biologists to set up. Therefore, we design an intuitive friendly user interface for the potential cloud server with GPUs. Use the user interface through network, we can send the input data to remote server without cumbersome setting in local host. Finally, we can receive the alignment results from the remote cloud server with GPUs.
Keywords :
biology computing; cloud computing; graphical user interfaces; graphics processing units; parallel architectures; parallel processing; CUDA; GPU-REMuSiC execution environment; GPU-based cloud service; computational biology; constrained multiple sequence alignment tools; domain knowledge; graphics processing units; regular expression constrains; remote cloud server; user friendly interface; user-specified residues; user-specified segments; Algorithm design and analysis; Biology; Cloud computing; Dynamic programming; Graphics processing units; Heuristic algorithms; Parallel algorithms; CUDA; GPUs; cloud computing; dynamic programming; graphics processing units; multiple sequence alignments; parallel processing; regular expression; user interface;
fLanguage :
English
Publisher :
ieee
Conference_Titel :
Cloud Computing Technology and Science (CloudCom), 2012 IEEE 4th International Conference on
Conference_Location :
Taipei
Print_ISBN :
978-1-4673-4511-8
Electronic_ISBN :
978-1-4673-4509-5
Type :
conf
DOI :
10.1109/CloudCom.2012.6427565
Filename :
6427565
Link To Document :
بازگشت