Title :
Parallelization of star alignment
Author :
Asril, Adi S. ; Kusuma, Wisnu A. ; Sukoco, Heru
Author_Institution :
Dept. of Comput. Sci., Bogor Agric. Univ., Bogor, Indonesia
Abstract :
Pair-wise sequence alignment is a technique of comparing the similarity of two organisms. It is the basic technique in DNA sequence alignment. There is an extraordinary number of data sequences when they are compared. Problems when comparing the huge data sequences are accuracy and efficiency. These parameters are contradiction which means reaching faster speed will decrease accuracy, and vice versa. Older method such as Needleman-Wunchs has extremely high computational complexity of O(n2). Similarly, multiple sequence alignment that processes the sequences one by one, called Star Alignment, takes time until O(k2n2). Therefore, they have a timing issue problem while processing the data. However, the computation result still has high accuracy. Consequently, it is very important to get a better way to improve the performance. One of the methods for increasing the speed is parallel computation by using multiple computers work together as a system. This research focuses on finding a faster method to process multiple sequence alignment using the Star method with a parallel computer. Our proposed method is implemented using Message Passing Interface (MPI). The results show that the paralellization of the Star Alignment increased speed up 4-6 times compared to that of using single CPU.
Keywords :
DNA; application program interfaces; biology computing; message passing; parallel processing; DNA sequence alignment; MPI; Star method; data sequences; message passing interface; multiple sequence alignment; pair-wise sequence alignment; parallel computation; parallel computer; star alignment parallelization; timing issue problem; Complexity theory; Computers; DNA; Information technology; Instruments; Parallel processing; Program processors; Multiple Sequence Alignment; Needlemen-Wunsch; Parallel Computing; Star Alignment;
Conference_Titel :
Instrumentation, Communications, Information Technology, and Biomedical Engineering (ICICI-BME), 2013 3rd International Conference on
Conference_Location :
Bandung
Print_ISBN :
978-1-4799-1649-8
DOI :
10.1109/ICICI-BME.2013.6698486