메뉴 건너뛰기




Volumn 69, Issue 10, 2009, Pages 854-865

Handling biological sequence alignments on networked computing systems: A divide-and-conquer approach

Author keywords

Biological sequences; Communication delay; Divisible load theory; Linear networks; Sequence alignment; Smith Waterman algorithm

Indexed keywords

BIOLOGICAL SEQUENCES; COMMUNICATION DELAY; DIVISIBLE LOAD THEORY; SEQUENCE ALIGNMENT; SMITH-WATERMAN ALGORITHM;

EID: 68849122267     PISSN: 07437315     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jpdc.2009.04.014     Document Type: Article
Times cited : (3)

References (35)
  • 1
    • 45449083047 scopus 로고    scopus 로고
    • Springer, Berlin
    • Adrianto W., Kwoh C.K., and Bertil S. Parallel DNA Sequence Alignment on the Cell Broadband Engine. LNCS vol. 4967/2008 (2008), Springer, Berlin 1249-1256
    • (2008) LNCS , vol.4967-2008 , pp. 1249-1256
    • Adrianto, W.1    Kwoh, C.K.2    Bertil, S.3
  • 6
    • 0026009526 scopus 로고
    • A novel randomized iteration strategy for aligning multiple protein sequences
    • Berger M.P., and Munson P.J. A novel randomized iteration strategy for aligning multiple protein sequences. Computer Applications in the Bioscience 7 (1991) 479-484
    • (1991) Computer Applications in the Bioscience , vol.7 , pp. 479-484
    • Berger, M.P.1    Munson, P.J.2
  • 10
    • 0007399046 scopus 로고    scopus 로고
    • Load partitioning and trade-off study for large matrix-vector computations in multicast bus networks with communication delays
    • Debasish D., and Kim H.J. Load partitioning and trade-off study for large matrix-vector computations in multicast bus networks with communication delays. Journal of Parallel and Distributed Computing 55 1 (1998) 32-59
    • (1998) Journal of Parallel and Distributed Computing , vol.55 , Issue.1 , pp. 32-59
    • Debasish, D.1    Kim, H.J.2
  • 11
    • 34547226808 scopus 로고    scopus 로고
    • On the design of high-performance algorithms for aligning multiple protein sequences on mesh-based multiprocessor architectures
    • Diana L.H., Bharadwaj V., and Bader D. On the design of high-performance algorithms for aligning multiple protein sequences on mesh-based multiprocessor architectures. Journal of Parallel and Distributed Computing 67 9 (2007) 1007-1017
    • (2007) Journal of Parallel and Distributed Computing , vol.67 , Issue.9 , pp. 1007-1017
    • Diana, L.H.1    Bharadwaj, V.2    Bader, D.3
  • 12
    • 68849106566 scopus 로고    scopus 로고
    • DNA Data Bank of Japan, http://www.ddbj.nig.ac.jp
  • 13
    • 14644430471 scopus 로고    scopus 로고
    • ProbCons: Probabilistic consistency-based multiple sequence alignment
    • Do C.B., Mahabhashyam M.S., Brudno M., and Batzoglou S. ProbCons: Probabilistic consistency-based multiple sequence alignment. Genome Research 15 2 (2005) 330-340
    • (2005) Genome Research , vol.15 , Issue.2 , pp. 330-340
    • Do, C.B.1    Mahabhashyam, M.S.2    Brudno, M.3    Batzoglou, S.4
  • 14
    • 3042666256 scopus 로고    scopus 로고
    • MUSCLE: Multiple sequence alignment with high accuracy and high throughput
    • Edgar R.C. MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nuclic Acids Research 32 5 (2004) 1792-1797
    • (2004) Nuclic Acids Research , vol.32 , Issue.5 , pp. 1792-1797
    • Edgar, R.C.1
  • 16
    • 68849091600 scopus 로고    scopus 로고
    • The EMBL (European Molecular Biology Laboratory) Nucleotide Sequence Database
    • The EMBL (European Molecular Biology Laboratory) Nucleotide Sequence Database, http://www.ebi.ac.uk/embl
  • 18
    • 68849090556 scopus 로고    scopus 로고
    • GenBank, http://www.ncbi.nlm.nih.gov
    • GenBank
  • 19
    • 0020484488 scopus 로고
    • An improved algorithm for matching biological sequences
    • Gotoh O. An improved algorithm for matching biological sequences. Journal of Molecular Biology 162 (1982) 705-708
    • (1982) Journal of Molecular Biology , vol.162 , pp. 705-708
    • Gotoh, O.1
  • 21
    • 0021919480 scopus 로고
    • Rapid and sensitive protein similarity searches
    • Lipman D.J., and Pearson W.R. Rapid and sensitive protein similarity searches. Science 227 (1985) 1435-1441
    • (1985) Science , vol.227 , pp. 1435-1441
    • Lipman, D.J.1    Pearson, W.R.2
  • 22
    • 0032945593 scopus 로고    scopus 로고
    • DiAlign 2: Improvement of the segment-to-segment approach to multiple sequence alignment
    • Morgenstern B. DiAlign 2: Improvement of the segment-to-segment approach to multiple sequence alignment. Bioinformatics 15 3 (1999) 211-218
    • (1999) Bioinformatics , vol.15 , Issue.3 , pp. 211-218
    • Morgenstern, B.1
  • 23
    • 0014757386 scopus 로고
    • A general method applicable to the search for similarities in the amino acid sequence of two sequences
    • Needleman S.B., and Wunsch C.D. A general method applicable to the search for similarities in the amino acid sequence of two sequences. Journal of Molecular Biology 48 (1970) 443-453
    • (1970) Journal of Molecular Biology , vol.48 , pp. 443-453
    • Needleman, S.B.1    Wunsch, C.D.2
  • 24
    • 0034623005 scopus 로고    scopus 로고
    • T-Coffee: A novel method for fast and accurate multiple sequence alignment
    • Notredame C., Higgins D.G., and Heringa J. T-Coffee: A novel method for fast and accurate multiple sequence alignment. Journal of Molecular Biology 302 1 (2000) 205-217
    • (2000) Journal of Molecular Biology , vol.302 , Issue.1 , pp. 205-217
    • Notredame, C.1    Higgins, D.G.2    Heringa, J.3
  • 25
    • 0025272240 scopus 로고
    • Rapid and sensitive sequence comparison with FASTA and FASTP
    • Pearson W.R. Rapid and sensitive sequence comparison with FASTA and FASTP. Methods in Enzymology 183 (1990) 63-98
    • (1990) Methods in Enzymology , vol.183 , pp. 63-98
    • Pearson, W.R.1
  • 27
    • 0000821965 scopus 로고
    • On the theory and computation of evolutionary distances
    • Sellers P.H. On the theory and computation of evolutionary distances. SIAM Journal of Applied Mathematics 26 (1974) 787-793
    • (1974) SIAM Journal of Applied Mathematics , vol.26 , pp. 787-793
    • Sellers, P.H.1
  • 28
  • 30
    • 29444435065 scopus 로고    scopus 로고
    • Aligning biological sequences on distributed bus networks: A divisible load scheduling approach
    • Wong H.M., and Bharadwaj V. Aligning biological sequences on distributed bus networks: A divisible load scheduling approach. IEEE Transactions on Information Technology in BioMedicine 9 4 (2005) 489-501
    • (2005) IEEE Transactions on Information Technology in BioMedicine , vol.9 , Issue.4 , pp. 489-501
    • Wong, H.M.1    Bharadwaj, V.2
  • 34
    • 68849088261 scopus 로고    scopus 로고
    • Parallel T-Coffee: A parallel multiple sequence aligner
    • J. Zola, X. Yang, S. Rospondek, S. Aluru, Parallel T-Coffee: A parallel multiple sequence aligner, in: Proc. of ISCA PDCS-2007, 2007, pp. 248-253
    • Proc. of ISCA , vol.PDCS-2007
    • Zola, J.1    Yang, X.2    Rospondek, S.3    Aluru, S.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.