Design and implementation of FPGA-based DNA sequence alignment accelerator
Basic Local Alignment Search Tool (BLAST) is a standard computer application that uses in the Bioinformatics field to search for sequence similarity in genomic databases. This project describes a FPGA-based hardware implementation which using a systolic array design architecture for Basic Local Alig...
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| Format: | Thesis |
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2013
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| Online Access: | http://eprints.uthm.edu.my/5504/ http://eprints.uthm.edu.my/5504/1/MOHD_FIKRI_BIN_CHE_HUSIN.pdf |
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| Summary: | Basic Local Alignment Search Tool (BLAST) is a standard computer application that uses in the Bioinformatics field to search for sequence similarity in genomic databases. This project describes a FPGA-based hardware implementation which using a systolic array design architecture for Basic Local Alignment Search Tool (BLAST). Before this designs detect at most one hit in one clock cycle, this design applies a Multiple Hits Detection Module which is a pipelining systolic array to search multiple hits in one clock cycle. This computationally intensive critical segment has been designed and implemented in the FPGA that runs on Cyclone II processor in the Altera DE 2 board. The concepts of portability, scalability and cost-effectiveness of the implementation are also demonstrated from the results obtained. |
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