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Volumn 23, Issue 7, 2015, Pages 1287-1300

Multicore SIMD ASIP for Next-Generation Sequencing and Alignment Biochip Platforms

Author keywords

Application specific instruction set architecture; biochip platforms; biological sequences alignment; multicore architecture; single instruction multiple data (SIMD).

Indexed keywords

ALIGNMENT; APPLICATION SPECIFIC INTEGRATED CIRCUITS; BIOCHIPS; BIOINFORMATICS; CMOS INTEGRATED CIRCUITS; FIELD PROGRAMMABLE GATE ARRAYS (FPGA); LOGIC SYNTHESIS; MEMORY ARCHITECTURE; MICROPROCESSOR CHIPS; PARALLEL PROCESSING SYSTEMS; SOFTWARE ARCHITECTURE;

EID: 85027933838     PISSN: 10638210     EISSN: None     Source Type: Journal    
DOI: 10.1109/TVLSI.2014.2333757     Document Type: Article
Times cited : (23)

References (30)
  • 2
    • 77952962769 scopus 로고    scopus 로고
    • Development of personalized tumor biomarkers using massively parallel sequencing
    • Feb.
    • R. J. Leary et al., "Development of personalized tumor biomarkers using massively parallel sequencing, " Sci. Transl. Med., vol. 2, no. 20, p. 20ra14, Feb. 2010.
    • (2010) Sci. Transl. Med. , vol.2 , Issue.20
    • Leary, R.J.1
  • 3
    • 84867835666 scopus 로고    scopus 로고
    • Integration of magnetoresistive biochips on a CMOS circuit, "
    • Nov.
    • F. A. Cardoso et al, "Integration of magnetoresistive biochips on a CMOS circuit, " IEEE Trans. Magn., vol. 48, no. 11, pp. 3784-3787, Nov. 2012.
    • (2012) IEEE Trans. Magn. , vol.48 , Issue.11 , pp. 3784-3787
    • Cardoso Et Al, F.A.1
  • 4
    • 67649610447 scopus 로고    scopus 로고
    • A portable and autonomous magnetic detection platform for biosensing
    • May
    • J. Germano et al., "A portable and autonomous magnetic detection platform for biosensing, " Sensors, vol. 9, no. 6, pp. 4119-4137, May 2009.
    • (2009) Sensors , vol.9 , Issue.6 , pp. 4119-4137
    • Germano, J.1
  • 5
    • 84874531575 scopus 로고    scopus 로고
    • Solid-state and biological nanopore for real-time sensing of single chemical and sequencing of DNA
    • Feb.
    • F. Haque, J. Li, H.-C. Wu, X.-J. Liang, and P. Guo, "Solid-state and biological nanopore for real-time sensing of single chemical and sequencing of DNA, " Nano Today, vol. 8, no. 1, pp. 56-74, Feb. 2013.
    • (2013) Nano Today , vol.8 , Issue.1 , pp. 56-74
    • Haque, F.1    Li, J.2    Wu, H.-C.3    Liang, X.-J.4    Guo, P.5
  • 6
    • 84862024420 scopus 로고    scopus 로고
    • Integrated hardware architecture for efficient computation of the n-best bio-sequence local alignments in embedded platforms, "
    • Jul.
    • N. Sebastião, N. Roma, and P. Flores, "Integrated hardware architecture for efficient computation of the n-best bio-sequence local alignments in embedded platforms, " IEEE Trans. Very Large Scale Integr. (VLSI) Syst, vol. 20, no. 7, pp. 1262-1275, Jul. 2012.
    • (2012) IEEE Trans. Very Large Scale Integr. (VLSI) Syst , vol.20 , Issue.7 , pp. 1262-1275
    • Sebastião, N.1    Roma, N.2    Flores, P.3
  • 7
    • 47349107082 scopus 로고    scopus 로고
    • Design and implementation of a highly parameterised FPGA-based skeleton for pairwise biological sequence alignment
    • Apr.
    • K. Benkrid, Y Liu, and A. Benkrid, "Design and implementation of a highly parameterised FPGA-based skeleton for pairwise biological sequence alignment, " in Proc. IEEE Symp. Field-Program. Custom Comput. Mach. (FCCM), Apr. 2007, pp. 275-278.
    • (2007) Proc. IEEE Symp. Field-Program. Custom Comput. Mach. (FCCM) , pp. 275-278
    • Benkrid, K.1    Liu, Y.2    Benkrid, A.3
  • 8
    • 57649226177 scopus 로고    scopus 로고
    • A reconfig-urable accelerator for Smith-Waterman algorithm, "
    • Dec.
    • X. Jiang, X. Liu, L. Xu, P. Zhang, and N. Sun, "A reconfig-urable accelerator for Smith-Waterman algorithm, " IEEE Trans. Circuits Syst. II: Exp. Briefs, vol. 54, no. 12, pp. 1077-1081, Dec. 2007.
    • (2007) IEEE Trans. Circuits Syst. II: Exp. Briefs , vol.54 , Issue.12 , pp. 1077-1081
    • Jiang, X.1    Liu, X.2    Xu, L.3    Zhang, P.4    Sun, N.5
  • 13
    • 0023989064 scopus 로고
    • Improved tools for biological sequence comparison
    • W R. Pearson and D. J. Lipman, "Improved tools for biological sequence comparison, " Proc. Nat. Acad. Sci., vol. 85, no. 8, pp. 2444-2448, 1988.
    • (1988) Proc. Nat. Acad. Sci. , vol.85 , Issue.8 , pp. 2444-2448
    • Pearson, W.R.1    Lipman, D.J.2
  • 14
    • 0014757386 scopus 로고
    • A general method applicable to the search for similarities in the amino acid sequence of two proteins
    • Mar.
    • S. B. Needleman and C. D. Wunsch, "A general method applicable to the search for similarities in the amino acid sequence of two proteins, " J. Molecular Biol., vol. 48, no. 3, pp. 443-453, Mar. 1970.
    • (1970) J. Molecular Biol. , vol.48 , Issue.3 , pp. 443-453
    • Needleman, S.B.1    Wunsch, C.D.2
  • 15
    • 0019887799 scopus 로고
    • Identification of common molecular subsequences
    • Mar.
    • T. F. Smith and M. S. Waterman, "Identification of common molecular subsequences, " J. Molecular Biol., vol. 147, no. 1, pp. 195-197, Mar. 1981.
    • (1981) J. Molecular Biol. , vol.147 , Issue.1 , pp. 195-197
    • Smith, T.F.1    Waterman, M.S.2
  • 16
    • 0020484488 scopus 로고
    • An improved algorithm for matching biological sequences
    • Dec.
    • O. Gotoh, "An improved algorithm for matching biological sequences, " J. Molecular Biol., vol. 162, no. 3, pp. 705-708, Dec. 1982.
    • (1982) J. Molecular Biol. , vol.162 , Issue.3 , pp. 705-708
    • Gotoh, O.1
  • 17
    • 0033743209 scopus 로고    scopus 로고
    • Six-fold speed-up of Smith-Waterman sequence database searches using parallel processing on common microprocessors
    • Mar.
    • T. Rognes and E. Seeberg, "Six-fold speed-up of Smith-Waterman sequence database searches using parallel processing on common microprocessors, " Bioinformatics, vol. 16, no. 8, pp. 699-706, Mar. 2000.
    • (2000) Bioinformatics , vol.16 , Issue.8 , pp. 699-706
    • Rognes, T.1    Seeberg, E.2
  • 18
    • 79957630864 scopus 로고    scopus 로고
    • Faster Smith-Waterman database searches with inter-sequence SIMD parallelisation
    • T. Rognes, "Faster Smith-Waterman database searches with inter-sequence SIMD parallelisation, " BMC Bioinform., vol. 12, no. 1, p. 221, 2011.
    • (2011) BMC Bioinform. , vol.12 , Issue.1
    • Rognes, T.1
  • 19
    • 33846697176 scopus 로고    scopus 로고
    • Striped Smith-Waterman speeds database searches six times over other SIMD implementations
    • M. Farrar, "Striped Smith-Waterman speeds database searches six times over other SIMD implementations, " Bioinformatics, vol. 23, no. 2, pp. 156-161, 2007.
    • (2007) Bioinformatics , vol.23 , Issue.2 , pp. 156-161
    • Farrar, M.1
  • 20
    • 0025950944 scopus 로고
    • Searching protein sequence libraries: Comparison of the sensitivity and selectivity of the Smith-Waterman and FASTA algorithms
    • Nov.
    • W R. Pearson, "Searching protein sequence libraries: Comparison of the sensitivity and selectivity of the Smith-Waterman and FASTA algorithms, " Genomics, vol. 11, no. 3, pp. 635-650, Nov. 1991.
    • (1991) Genomics , vol.11 , Issue.3 , pp. 635-650
    • Pearson, W.R.1
  • 21
    • 0030935244 scopus 로고    scopus 로고
    • Using video-oriented instructions to speed up sequence comparison
    • A. Wozniak, "Using video-oriented instructions to speed up sequence comparison, " Comput. Appl. Biosci., vol. 13, no. 2, pp. 145-150, 1997.
    • (1997) Comput. Appl. Biosci. , vol.13 , Issue.2 , pp. 145-150
    • Wozniak, A.1
  • 22
    • 72849144434 scopus 로고    scopus 로고
    • Sequencing technologies-The next generation
    • Jan.
    • M. L. Metzker, "Sequencing technologies-The next generation, " Nature Rev. Genet., vol. 11, no. 1, pp. 31-46, Jan. 2010.
    • (2010) Nature Rev. Genet. , vol.11 , Issue.1 , pp. 31-46
    • Metzker, M.L.1
  • 23
    • 85028222639 scopus 로고    scopus 로고
    • Intel 64 and IA-32 Architectures Software Developer's Manual
    • Feb.
    • Intel 64 and IA-32 Architectures Software Developer's Manual. Santa Clara, CA, USA: Intel, Feb. 2013.
    • (2013) Santa Clara, CA, USA: Intel
  • 24
    • 77953085846 scopus 로고    scopus 로고
    • MB-LITE: A robust, lightweight soft-core implementation of the MicroBlaze architecture
    • Mar.
    • T. Kranenburg and R. van Leuken, "MB-LITE: A robust, lightweight soft-core implementation of the MicroBlaze architecture, " in Proc. Design, Autom. Test Eur. Conf. Exhibit. (DATE), Mar. 2010, pp. 997-1000.
    • (2010) Proc. Design, Autom. Test Eur. Conf. Exhibit. (DATE) , pp. 997-1000
    • Kranenburg, T.1    Van Leuken, R.2
  • 27
    • 77952682294 scopus 로고    scopus 로고
    • Quantitative analysis of sequence alignment applications on multiprocessor architectures
    • F. S. Castaño, A. Ramirez, and M. Valero, "Quantitative analysis of sequence alignment applications on multiprocessor architectures, " in Proc. ACM Conf. Comput. Frontiers, 2009, pp. 61-70.
    • (2009) Proc. ACM Conf. Comput. Frontiers , pp. 61-70
    • Castaño, F.S.1    Ramirez, A.2    Valero, M.3
  • 28
    • 84873448750 scopus 로고    scopus 로고
    • System-level prototyping framework for heterogeneous multi-core architecture applied to biological sequence analysis
    • Oct.
    • N. Roma and P. Magalhaes, "System-level prototyping framework for heterogeneous multi-core architecture applied to biological sequence analysis, " in Proc. IEEE Int. Symp. Rapid Syst. Prototyping (RSP), Oct. 2012, pp. 156-162.
    • (2012) Proc. IEEE Int. Symp. Rapid Syst. Prototyping (RSP) , pp. 156-162
    • Roma, N.1    Magalhaes, P.2
  • 30
    • 84879413445 scopus 로고    scopus 로고
    • Configurable and scalable class of high performance hardware accelerators for simultaneous DNA sequence alignment
    • Jul.
    • N. Sebastião, N. Roma, and P. Flores, "Configurable and scalable class of high performance hardware accelerators for simultaneous DNA sequence alignment, " Concurrency Comput., Pract. Exper., vol. 25, no. 10, pp. 1319-1339, Jul. 2013.
    • (2013) Concurrency Comput., Pract. Exper. , vol.25 , Issue.10 , pp. 1319-1339
    • Sebastião, N.1    Roma, N.2    Flores, P.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.