DocumentCode :
139016
Title :
Sequence alignment using systolic array for an accelerator
Author :
Razip, Mansur Iylia Mohamed ; Al Junid, Syed Abdul Mutalib ; Halim, Abdul Karimi ; Majid, Zulkifli Abd
Author_Institution :
Fac. of Electr. Eng., Univ. Teknol. Mara, Shah Alam, Malaysia
fYear :
2014
fDate :
24-25 March 2014
Firstpage :
663
Lastpage :
665
Abstract :
Performance and large memory space are the most prominent issues highlighted for local DNA sequences alignment. Therefore, this study is an attempt to test the systolic array approach for Smith-Waterman (SW) algorithm for improving the performance of DNA sequence alignment accelerator. The design was developed using LabVIEW and targeted to Xilinx Spartan 3E while the original SW has been used as a benchmark for performance comparison. Systolic array SW has recorded better performance as compared to original SW. Thus, by applying systolic array concept, it will improve the alignment performance whilst minimize the complexity of the design.
Keywords :
DNA; digital circuits; field programmable gate arrays; logic design; sequences; systolic arrays; DNA sequence alignment accelerator; LabVIEW; Smith-Waterman algorithm; Xilinx Spartan 3E; memory space; systolic array; Algorithm design and analysis; Arrays; Conferences; DNA; Microprocessors; Optimization; DNA; FPGA; Smith-Waterman; bioinformatics; sequence alignment; systolic;
fLanguage :
English
Publisher :
ieee
Conference_Titel :
Power Engineering and Optimization Conference (PEOCO), 2014 IEEE 8th International
Conference_Location :
Langkawi
Print_ISBN :
978-1-4799-2421-9
Type :
conf
DOI :
10.1109/PEOCO.2014.6814510
Filename :
6814510
Link To Document :
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