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Volumn 16, Issue 12, 2008, Pages 1666-1676

A special-purpose architecture for solving the breakpoint median problem

Author keywords

Bioinformatics; Computational biology; Field programmable gate array (FPGA); Phylogenetic reconstruction; Reconfigurable computing

Indexed keywords

BIOINFORMATICS; COMBINATORIAL MATHEMATICS; COMBINATORIAL OPTIMIZATION; LOGIC GATES; REPAIR; RESTORATION;

EID: 56749092988     PISSN: 10638210     EISSN: None     Source Type: Journal    
DOI: 10.1109/TVLSI.2008.2001298     Document Type: Article
Times cited : (10)

References (29)
  • 3
    • 33749041882 scopus 로고    scopus 로고
    • Biomolecular simulations on petascale: Promises and challenges
    • 46, pp
    • P. K. Agarwal and S. R. Alam, "Biomolecular simulations on petascale: Promises and challenges," in J. Phys.: Conf. Series, 9, 2006, vol. 46, pp. 327-333.
    • (2006) J. Phys.: Conf. Series , vol.9 , pp. 327-333
    • Agarwal, P.K.1    Alam, S.R.2
  • 4
    • 47349085305 scopus 로고    scopus 로고
    • R. Sass, W. Kritikos, A. Schmidt, S. Beeravolu, P. Beeraka, K. Datta, D. Andrews, R. Miller, and D. Stanzione, Jr. Reconfigurable computing cluster (RCC) project: Investigating the feasibility of FPGA-based petascale computing, in Proc. IEEE Symp. Field Program. Custom Comput. Mach., Apr. 2007, pp. 127-138.
    • R. Sass, W. Kritikos, A. Schmidt, S. Beeravolu, P. Beeraka, K. Datta, D. Andrews, R. Miller, and D. Stanzione, Jr. "Reconfigurable computing cluster (RCC) project: Investigating the feasibility of FPGA-based petascale computing," in Proc. IEEE Symp. Field Program. Custom Comput. Mach., Apr. 2007, pp. 127-138.
  • 5
    • 34548246070 scopus 로고    scopus 로고
    • Is high-performance, reconfigurable computing the next supercomputing paradigm?
    • presented at the, SC, Tampa, FL
    • T. El-Ghazawi, "Is high-performance, reconfigurable computing the next supercomputing paradigm?," presented at the ACM/IEEE Supercomput. Conf. (SC), Tampa, FL, 2006.
    • (2006) ACM/IEEE Supercomput. Conf
    • El-Ghazawi, T.1
  • 6
    • 56749084994 scopus 로고    scopus 로고
    • 2007 [Online], Available: http://www.cray.com
    • 2007 [Online], Available: http://www.cray.com
  • 7
    • 34548442821 scopus 로고    scopus 로고
    • A general reconfigurable architecture for the BLAST algorithm
    • Sep
    • E. Sotiriades and A. Dollas, "A general reconfigurable architecture for the BLAST algorithm." J. VLSI Signal Process., vol. 48, no. 3, pp. 189-208, Sep. 2007.
    • (2007) J. VLSI Signal Process , vol.48 , Issue.3 , pp. 189-208
    • Sotiriades, E.1    Dollas, A.2
  • 9
    • 24044471657 scopus 로고    scopus 로고
    • Using reconfigurable hardware to accelerate multiple sequence alignment with ClustalW
    • T. Oliver, B. Schmidt, D. Nathan, R. Clemens, and D. Maskell, "Using reconfigurable hardware to accelerate multiple sequence alignment with ClustalW," Bioinformatics, vol. 21. no. 16, pp. 3431-3432, 2005.
    • (2005) Bioinformatics , vol.21 , Issue.16 , pp. 3431-3432
    • Oliver, T.1    Schmidt, B.2    Nathan, D.3    Clemens, R.4    Maskell, D.5
  • 10
    • 11144267902 scopus 로고    scopus 로고
    • Accelerating phylogenetics computing on the desktop: Experiments with executing UPGMA in programmable logic
    • J. P. Davis, S. Akella, and P. H. Waddell, "Accelerating phylogenetics computing on the desktop: Experiments with executing UPGMA in programmable logic," in Proc. 26th Annu. Int. Conf. IEEE Eng. Med. Biol. Soc. (IEMBS), 2004, pp. 2864-2868.
    • (2004) Proc. 26th Annu. Int. Conf. IEEE Eng. Med. Biol. Soc. (IEMBS) , pp. 2864-2868
    • Davis, J.P.1    Akella, S.2    Waddell, P.H.3
  • 11
    • 0029993075 scopus 로고    scopus 로고
    • Parametric genome rearrangement
    • M. Blanchette, T. Kunisawa, and D. Sankoff, "Parametric genome rearrangement," Gene, vol. 172, pp. GC11-GC17, 1996.
    • (1996) Gene , vol.172
    • Blanchette, M.1    Kunisawa, T.2    Sankoff, D.3
  • 12
    • 0036143403 scopus 로고    scopus 로고
    • Genome-scale evolution: Reconstructing gene orders in the ancestral species
    • G. Bourque and P. Pevzner, "Genome-scale evolution: Reconstructing gene orders in the ancestral species," Genome Res., vol. 12, pp. 26-36, 2002.
    • (2002) Genome Res , vol.12 , pp. 26-36
    • Bourque, G.1    Pevzner, P.2
  • 13
    • 0034767147 scopus 로고    scopus 로고
    • A fast linear-time algorithm for inversion distance with an experimental comparison
    • D. A. Bader, B. M. E. Moret, and M. Yan, "A fast linear-time algorithm for inversion distance with an experimental comparison," J. Comput. Biol., vol. 85, pp. 483-491. 2001.
    • (2001) J. Comput. Biol , vol.85 , pp. 483-491
    • Bader, D.A.1    Moret, B.M.E.2    Yan, M.3
  • 15
    • 23844520968 scopus 로고    scopus 로고
    • Steps toward accurate reconstructions of phylogenies from gene-order data
    • B. M. E. Moret, J. Tang, L.-S. Wang, and T. Warnow, "Steps toward accurate reconstructions of phylogenies from gene-order data," Comput. Syst. Sci., vol. 65, no. 3, pp. 508-525, 2002.
    • (2002) Comput. Syst. Sci , vol.65 , Issue.3 , pp. 508-525
    • Moret, B.M.E.1    Tang, J.2    Wang, L.-S.3    Warnow, T.4
  • 16
    • 19544394896 scopus 로고    scopus 로고
    • Reconstructing phylogenies from gene-content and gene-order data
    • O. Gascuel, Ed. Oxford. U.K, Oxford Univ. Press
    • B. M. E. Moret, J. Tang, and T. Warnow, "Reconstructing phylogenies from gene-content and gene-order data," in Mathematics of Evolution and Phylogeny, O. Gascuel, Ed. Oxford. U.K.: Oxford Univ. Press, 2005, pp. 321-352.
    • (2005) Mathematics of Evolution and Phylogeny , pp. 321-352
    • Moret, B.M.E.1    Tang, J.2    Warnow, T.3
  • 17
    • 0032746022 scopus 로고    scopus 로고
    • Disk-covering, a fast converging method for phylogenetic tree reconstruction
    • D. Huson, S. Nettles, and T. Warnow, "Disk-covering, a fast converging method for phylogenetic tree reconstruction," J. Comput. Biol., vol. 6, no. 3, pp. 369-386, 1999.
    • (1999) J. Comput. Biol , vol.6 , Issue.3 , pp. 369-386
    • Huson, D.1    Nettles, S.2    Warnow, T.3
  • 19
    • 0023375195 scopus 로고
    • The neighbor-joining method: A new method for reconstrucing phylogenetic trees
    • N. Saitou and N. Nei, "The neighbor-joining method: A new method for reconstrucing phylogenetic trees," Mol. Biol. Evol., vol. 4, pp. 406-425, 1987.
    • (1987) Mol. Biol. Evol , vol.4 , pp. 406-425
    • Saitou, N.1    Nei, N.2
  • 20
    • 56749142398 scopus 로고    scopus 로고
    • M. Blanchette, G. Bourque, and D. Sankoff, Breakpoint phytogenies, in Genome Informatics 1997, S. Miyano, T. Takagi, and editors. Eds. Tokyo: Univ. Academy Press, 1997, pp. 25-34.
    • M. Blanchette, G. Bourque, and D. Sankoff, "Breakpoint phytogenies," in Genome Informatics 1997, S. Miyano, T. Takagi, and editors. Eds. Tokyo: Univ. Academy Press, 1997, pp. 25-34.
  • 21
    • 0036143403 scopus 로고    scopus 로고
    • Genome-scale evolution: Reconstructing gene orders in the ancestral species
    • G. Bourque and P. Pevzner, "Genome-scale evolution: Reconstructing gene orders in the ancestral species." Genome Res., vol. 12, pp. 26-36, 2002.
    • (2002) Genome Res , vol.12 , pp. 26-36
    • Bourque, G.1    Pevzner, P.2
  • 22
    • 4544280334 scopus 로고    scopus 로고
    • The median problems for breakpoints are {NP}-complete
    • I. Pe'er and R. Shamir, "The median problems for breakpoints are {NP}-complete," Elec. Colloq. Comput. Complexity, vol. 71, 1998.
    • (1998) Elec. Colloq. Comput. Complexity , vol.71
    • Pe'er, I.1    Shamir, R.2
  • 25
    • 84947921171 scopus 로고
    • A hardware genetic algorithm for the traveling salesman problem on splash 2
    • Oxford. U.K, Aug
    • P. Graham and B. Nelson, "A hardware genetic algorithm for the traveling salesman problem on splash 2," in Proc. 5th Int. Workshop Field Program. Logic Appl. Oxford. U.K., Aug. 1995, pp. 352-361.
    • (1995) Proc. 5th Int. Workshop Field Program. Logic Appl , pp. 352-361
    • Graham, P.1    Nelson, B.2
  • 26
    • 47649095178 scopus 로고    scopus 로고
    • FPGA-Based implementation of genetic algorithm for the traveling salesman problem and its industrial application
    • Cairns, Australia, Jun
    • I. Skliarova and A. B. Ferrari. "FPGA-Based implementation of genetic algorithm for the traveling salesman problem and its industrial application," in Proc. Appl. Artif. Intell. Expert Syst. (IEA/AIE), Cairns, Australia, Jun. 2002, pp. 19-34.
    • (2002) Proc. Appl. Artif. Intell. Expert Syst. (IEA/AIE) , pp. 19-34
    • Skliarova, I.1    Ferrari, A.B.2
  • 28
    • 47649117565 scopus 로고    scopus 로고
    • FPGA acceleration of phylogeny reconstruction for whole genome data
    • presented at the, Boston, MA. Oct
    • J. D. Bakos, P. E. Elenis, and J. Tang, "FPGA acceleration of phylogeny reconstruction for whole genome data." presented at the 7th IEEE Int. Symp. Bioinform. Bioeng., Boston, MA. Oct. 2007.
    • (2007) 7th IEEE Int. Symp. Bioinform. Bioeng
    • Bakos, J.D.1    Elenis, P.E.2    Tang, J.3
  • 29
    • 46649120347 scopus 로고    scopus 로고
    • Inferring genome-scale rearrangement phytogeny and ancestral gene order: A Drosophila case study
    • A. Bhutkar, W. M. Gelbart, and T. F. Smith, "Inferring genome-scale rearrangement phytogeny and ancestral gene order: A Drosophila case study," Genome Biol., vol. 8, pp. R236-R236, 2007.
    • (2007) Genome Biol , vol.8
    • Bhutkar, A.1    Gelbart, W.M.2    Smith, T.F.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.