Sequence alignment using systolic array for an accelerator

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 wa...

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Bibliographic Details
Main Authors: Razip, Mansur Iylia Mohamed, Al Junid, Syed Abdul Mutalib, Halim, Abdul Karimi, Majid, Zulkifli Abd
Format: Conference Proceeding
Language:English
Subjects:
Algorithm design and analysis
Arrays
bioinformatics
Conferences
DNA
FPGA
Microprocessors
Optimization
sequence alignment
Smith-Waterman
systolic
Online Access:Request full text
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Summary: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.
DOI:10.1109/PEOCO.2014.6814510