FPGA-based hardware acceleration for local complexity analysis of massive genomic data

Integration, the VLSI Journal

Volumn 46, Issue 3, 2013, Pages 230-239

  Papadopoulos, Agathoklis ^a   Kirmitzoglou, Ioannis ^a   Promponas, Vasilis J ^a   Theocharides, Theocharis ^a  

^a UNIVERSITY OF CYPRUS   (Cyprus)

Author keywords

Bioinformatics; Genomics; Hardware acceleration; Reconfigurable parallel architectures

Indexed keywords

ACCELERATOR ARCHITECTURES; FPGA-BASED ACCELERATIONS; GENOMICS; HARDWARE ACCELERATION; MULTI-THREADED IMPLEMENTATION; PROTEIN SEQUENCE ANALYSIS; RECONFIGURABLE; SEQUENCE LENGTH DISTRIBUTIONS;

ACCELERATION; BENCHMARKING; BIOINFORMATICS; COMPUTER HARDWARE; ENERGY EFFICIENCY; GENES; HARDWARE; MICROPROCESSOR CHIPS; PARALLEL ARCHITECTURES; RECONFIGURABLE HARDWARE;

CLUSTERING ALGORITHMS;

EID: 84878019185     PISSN: 01679260     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.vlsi.2012.10.003     Document Type: Article

References (32)

1. M.L. Metzker Sequencing technologies - the next generation Nature Reviews Genetics 11 1 2008 31 46
2. E.R. Mardis Anticipating the $1000 genome Genome Biology 7 112 2006
3. R. Nair, and B. Rost Sequence conserved for subcellular localization Protein Science 11 12 2002 2836 2847
4. A.J. Enright, S. van Dongen, and C.A. Ouzounis An efficient algorithm for large-scale detection of protein families Nucleic Acids Research 30 7 2002 1575 1884
5. A.E. Darling, L. Carey, and W. Feng-chun The design, implementation, and evaluation of mpiBLAST ClusterWorld 2003 13 15
6. A. Gara Overview of the Blue Gene/L system architecture IBM Journal of Research and Development 49 2 2005 195 212
7. P. Vouzis, and N. Sahinidis GPU-BLAST: using graphics processors to accelerate protein sequence alignment Bioinformatics 27 2010 182 188
8. C. Fletcher, I. Lebedev, N. Asadi, D. Burke, J. Wawrzynek, Bridging the GPGPU-FPGA efficiency gap, in: Proceedings of the 19th ACM/SIGDA International Symposium on Field Programmable Gate Arrays (FPGA 11), New York, 2011.
9. J. Fowers, G.Brown, P.Cooke, G. Stitt, A performance and energy comparison of FPGAs, GPUs, and multicores for sliding-window applications, in: Proceedings of the ACM/SIGDA International Symposium on Field Programmable Gate Arrays, New York, 2012.
10. S. Sarkar, G.R. Kulkarni, P.P. Pande, and A. Kalyanaraman Network-on-chip hardware accelerators for biological sequence alignment IEEE Transactions on Computers 59 1 2010 29 41
11. S. Karlin, and S.F. Altschul Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes Proceedings of the National Academy of Sciences of the United States of America 87 6 1990 2264 2268
12. J.C. Wootton Sequences with 'unusual' amino acid compositions Current Opinion in Structural Biology 4 1994 413 421
13. J.C. Wootton, and S. Federhen Statistics of local complexity in amino acid sequences and sequence databases Computers and Chemistry 17 2 1993 149 163
14. W. Haerty, and G.B. Golding Low-complexity sequences and single amino acid repeats: not just 'junk' peptide sequences Genome 53 2010 753 762
15. V.J. Promponas CAST: an iterative algorithm for the complexity analysis of sequence tracts Bioinformatics 16 10 2000 915 922
16. D. Benton Genbank Nucleic Acids Research 40 2012 D48 D53
17. A. Papadopoulos, V.J. Promponas, T. Theocharides, Towards systolic hardware acceleration for local complexity analysis of massive genomic data, in: Proceedings of the ACM/IEEE Great Lakes Symposium on VLS(GLSVLSI 2012), Salt Lake City, 2012, 10.1145/2206781.2206864.
18. S.F. Altschul Basic local alignment search tool Journal of Molecular Biology 215 3 1990 403 410
19. S.F. Altschul Gapped BLAST and PSI-BLAST: a new generation of protein database search programs Nucleic Acids Research 25 17 1997 3389 3402
20. 〈http://www.scopus.com〉, September 2012.
21. R.C. Edgar Search and clustering orders of magnitude faster than BLAST Bioinformatics (Oxford, England) 26 19 2010 2460 2461
22. M. Herbordt, J. Model, B. Sukhwani, Y. Gu, and T. Van Court Single pass streaming BLAST on FPGAs Parallel Computing Journal 48 3 2007 189 208
23. E. Sotiriades, and A. Dollas A General reconfigurable architecture for the BLAST algorithm Journal of VLSI Signal Processing Systems for Signal, Image, and Video Technology 48 3 2007 189 208
24. S. Kasap, K. Benkrid, Y. Liu, A high performance FPGA-based implementation of position specific iterated blast, in: Proceedings of the ACM/SIGDA International Symposium on Field Programmable Gate Arrays, FPGA 09, 2009.
25. J. Garnier, J. Gibrat, and B. Robson GOR method for predicting protein secondary structure from amino acid sequence Methods in Enzymology 266 1996 540 553
26. F. Xia, Y. Dou, G. Lei, and Y. Tan FPGA accelerator for protein secondary structure prediction based on the GOR algorithm BMC Bioinformatics 12 Suppl. 1 2011 S5
27. P. Afratis, E. Sotiriades, G. Chrysos, S. Fytraki, D. Pnevmatikatos, A rate-based prefiltering approach to blast acceleration, in: Proceedings of the International Conference on Field Programmable Logic and Applications, 2008.
28. 〈http://www.ncbi.nlm.nih.gov/〉, September 2012.
29. Xilinx, Available from: 〈http://www.xilinx.com/support/ documentation/ip-documentation/pcie-blk-plus-ug341.pdf/〉, September 2012.
30. Xilinx, Available from: 〈http://www.xilinx.com/support/ documentation/ip-documentation/fifo-generator-ug175.pdf〉, September 2012.
31. 〈http://www.dna.affrc.go.jp/misc/MPsrch/InfoIUPAC.html〉, September 2012.
32. Dryad Digital Repository, Available from: 〈http://www.datadryad.org/ 〉, September 2012.