The accelerating implementation of BLAST with stream processor

Proceeding 2009 IEEE 10th International Conference on Computer-Aided Industrial Design and Conceptual Design: E-Business, Creative Design, Manufacturing - CAID and CD'2009

Volumn , Issue , 2009, Pages 2245-2250

  Wei, Gang ^a   Ma, Chao ^a   Pei, Songwen ^b   Wu, Baifeng ^a  

^a FUDAN UNIVERSITY   (China)

^b UNIVERSITY OF SHANGHAI FOR SCIENCE AND TECHNOLOGY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

MAIN TASKS; SEQUENCE ALIGNMENTS; STREAM PROCESSOR;

ALIGNMENT; BIOINFORMATICS; COMPUTER GRAPHICS EQUIPMENT; CONCEPTUAL DESIGN; PRODUCT DESIGN; RADIO TELESCOPES;

ELECTRONIC COMMERCE;

EID: 77949705936     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/CAIDCD.2009.5375228     Document Type: Conference Paper

References (13)

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3. W. Pearson. Rapid and sensitive sequence comparison with fastp and fasta. Methods Enzymol, 183:63-98, 1990.
4. National Center for Biological Information, Growth of GenBank, 2002, http://www.ncbi.nlm. nih.gov/Genbank/genbankstats.html.
5. Jacob, A., Lancaster, J., et al.: FPGA-accelerated seed generation in Mercury BLASTP. In: Proc. 15th Annual IEEE Symposium on Field-Programmable Custom Computing Machines, pp. 95-106, 2007.
6. Muriki, K., Underwood, K.D., et al.: RC-BLAST: Towards a Portable, Cost-Effective Open Source Hardware Implementation. In: Proc. 19th IEEE International Parallel and Distributed Processing Symposium, 2005.
7. Lavenier, D., Xinchun, L., Georges, G.: Seed-based Genomic Sequence Comparison using a FPGA/FLASH Accelerator. In: IEEE International Conference on Field Programmable Technology, pp. 41-48, 2006.
8. Chang, C.: BLAST Implementation on BEE2. Electrical Engineering and Computer Science University of California at Berkeley, 2005.
9. CLC Desktop Hardware-Acceleration. White paper on CLC Bioinformatics Cube, 2006.
10. Mitrion.Inc.: NCBI BLAST Accelerator 2007, http://www.mitrionics.com, available in June 2009.
11. mpiBLAST. http://www.mpiblast.org/, available in June 2009.
12. Chao-Tung Yang, Tsu-Fen Han and Heng-Chuan Kan. G-BLAST: a Grid-based solution for mpiBLAST on computational Grids. Concurrency Computation: Pract. Exper. 21:225-255, 2009.
13. AMD Inc. Stream Computing User Guide. http://ati.amd.com, available in June 2009.