Hardware BLAST algorithms with multi-seeds detection and parallel extension

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 4943 LNCS, Issue , 2008, Pages 39-50

  Xia, Fei ^a   Dou, Yong ^a   Xu, Jinbo ^a  

^a NATIONAL UNIVERSITY OF DEFENSE TECHNOLOGY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

AGRICULTURAL PRODUCTS; CAVITY RESONATORS; DATA STORAGE EQUIPMENT; EXPLOSIVES; FIELD PROGRAMMABLE GATE ARRAYS (FPGA); HEURISTIC PROGRAMMING; PARALLEL ALGORITHMS; PIPELINES; RADIO TELESCOPES;

BLAST ALGORITHM; CLOCK FREQUENCIES; FPGA IMPLEMENTATIONS; MEMORY RESOURCES; PROCESSING ELEMENTS; RE-CONFIGURABLE COMPUTING; SUB-STRINGS; SUPERIOR PERFORMANCE; TWO STAGES;

SEED;

EID: 52049086045     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-540-78610-8_7     Document Type: Conference Paper

References (22)

1. Altschul, S.F., Gish, W., et al.: Basic local alignment search tool. Molecular Biology, 403-410 (1990)
2. NCBI, GenBank Growth Statistics (2006), http://www.ncbi.nlm.nih.gov/ Genbank/genbankstats.html
3. Buhler, J.D., Lancaster, J.M., et al.: Mercury BLASTN: Faster DNA Sequence Comparison Using a Streaming Hardware Architecture. In: Proc. 3rd Annual Re-configurable Systems Summer Institute (2007)
4. Krishnanurthy, P., Buhler, J., et al.: Biosequence Similarity search on the Mercury system. In: Proc. 15th IEEE International Conference on Application-Specific Systems, Architectures and Processors, pp. 365-375 (2004)
5. Lancaster, J., Buhler, J., et al.: Acceleration of Ungapped Extension in Mercury BLAST. In: Proc. 7th Workshop on Media and Streaming Processors, pp. 50-57 (2005)
6. Herbordt, M.C., Model, J., et al.: Single Pass, BLAST-Like, Approximate String Matching on FPGAs. In: Proc. 14th Annual IEEE Symposium on Field-Programmable Custom Computing Machines, pp. 217-226 (2006)
7. 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)
8. 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)
9. 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)
10. Sotiriades, E., Dollas, A.: Design Space Exploration for the BAST Algorithm Implementation. In: Proc. 15th Annual IEEE Symposium on Field-Programmable Custom Computing Machines (2007)
11. Sotiriades, E., Kozanitis, C, Dollas, A.: FPGA based Architecture for DNA Sequence Comparison and Database Search. In: Proc. 20th IEEE International Parallel and Distributed Processing Symposium (2006)
12. Chang, C: BLAST Implementation on BEE2. Electrical Engineering and Computer Science University of California at Berkeley (2005) , http://bee2.eecs.berkeley.edu
13. CLC Desktop Hardware-Acceleration. White paper on CLC Bioinformatics Cube (2006), http://www.clccube.com
14. Mitrion.Inc: NCBI BLAST Accelerator (2007), http://www.mitrionics.com
15. Timelogic.Inc: Timelogic DeCypher BLAST Engine (2006), http://www.timelogic.com/decypher_blast.html
16. Hoang, D., et al.: FPGA Implementation of Systolic Sequence Alignment. In: Proc. 2nd International Workshop on Field-Programmable Logic and Applications, Lecture Notes in Computer Science, pp. 183-191 (1992)
17. Hoang, D., et al.: Searching Genetic Databases on Splash2. In: Proc. IEEE Workshop on FPGAs for Custom Computing Machines, pp. 185-191 (1993)
18. Guccione, S.A., Keller, E.: Gene Matching Using JBits. In: Glesner, M., Zipf, P., Renovell, M. (eds.) FPL 2002. LNCS, vol. 2438, Springer, Heidelberg (2002)
19. Oliver, T., et al.: Hyper Customized Processors for Bio-Sequence Database Scanning on FPGAs. In: Proc. ACM/SIGDA 13th international symposium on Field programmable gate arrays, pp. 229-237 (2005)
20. Court, T.V., Herbordt, M.C.: Families of FPGA-Based Accelerators for Approximate String Matching. Microprocessors and Microsystems 31, 135-145 (2007)
21. NCBI BLAST Database, National Center for Biotechnology Information (2006), http://www.ncbi.nih.gov/BLAST
22. EBI, European Bioinformatics Institute (2007), http://www.ebi.ac.uk/ uniprot/database/download.html