A rate-based prefiltering approach to blast acceleration

Proceedings - 2008 International Conference on Field Programmable Logic and Applications, FPL

Volumn , Issue , 2008, Pages 631-634

  Afratis, Panagiotis ^a   Sotiriades, Euripides ^a   Chrysos, Grigorios ^a   Fytraki, Sotiria ^a   Pnevmatikatos, Dionisios ^a  

^a TECHNICAL UNIVERSITY OF CRETE   (Greece)

Author keywords

[No Author keywords available]

Indexed keywords

EXPLOSIVES; NUCLEIC ACIDS; ORGANIC ACIDS; RADIO TELESCOPES; SEARCH ENGINES;

DATABASE SEARCHES; DNA SEQUENCE COMPARISONS; ORDERS OF MAGNITUDES; PREFILTERING; PREFILTERING APPROACHES; PREPROCESSOR; RECONFIGURABLE; RECONFIGURABLE HARDWARES; SIGNIFICANT REDUCTIONS;

DATABASE SYSTEMS;

EID: 54949126013     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/FPL.2008.4630026     Document Type: Conference Paper

References (7)

1. K. Muriki, K. Underwood and R Sass, RC-BLAST: Towards an open source hardware implementation, in Proceedings of the International Workshop on High Performance Computational Biology, Denver, 2005
2. M. C. Herbordt, J. Model, Y. Gu, B. Sukhwani, T. VanCourt, "Single Pass, BLAST-Like, Approximate String Matching on FPGAs", in Proceedings of 14th Annual IEEE Symposium on Field-Programmable Custom Computing Machines (FCCM'06), pp. 217-226, 2006.
3. D. Lavenier, G. Georges, L. Xinchun, "A Reconfigurable Index FLASH Memory tailored to Seed-Based Genomic Sequence Comparison Algorithms". The Journal of VLSI Signal Processing Systems for Signal, Image, and Video Technology, Special Issue on Computing Architectures and Acceleration for Bioinformatics Algorithms, Kluwer Academic Publishers Volume 48, Issue 3 Pages: 255 -269, September, 2007.
4. E. Sotiriades, A. Dollas "A General Reconfigurable Architecture for the BLAST algorithm". The Journal of VLSI Signal Processing Systems for Signal, Image, and Video Technology, Special Issue on Computing Architectures and Acceleration for Bioinformatics Algorithms, Kluwer Academic Publishers Volume 48, Issue 3 Pages: 189-208, September, 2007.
5. A. Jacob, J. Lancaster, J. Buhler, R. D. Chamberlain, "FPGA-accelerated seed generation in Mercury BLASTP," Field-Programmable Custom Computing Machines, 2007, FCCM 2007. 15th Annual IEEE Symposium on , vol., no., pp.95-106, 23-25 April 2007
6. C. Chang, BBLAST Implementation on BEE2, University of California at Berkeley, California, 2004.
7. www.ncbi.nlm.nih.gov