메뉴 건너뛰기




Volumn 3, Issue 1, 2011, Pages 57-63

A comparative analysis of parallel computing approaches for genome assembly

Author keywords

genome assembly; isoefficiency; parallel computing; sequencing

Indexed keywords

ALGORITHM; ARTICLE; BIOLOGY; COMPARATIVE STUDY; DNA SEQUENCE; EVALUATION; GENOME; GENOMICS; INFORMATION PROCESSING; METHODOLOGY;

EID: 84858767001     PISSN: 19132751     EISSN: 18671462     Source Type: Journal    
DOI: 10.1007/s12539-011-0062-0     Document Type: Article
Times cited : (4)

References (21)
  • 2
    • 33750953227 scopus 로고    scopus 로고
    • Whole-genome re-sequencing
    • Bentley, D. 2006. Whole-genome re-sequencing. Curr Opin Genet Dev 16, 545-552.
    • (2006) Curr Opin Genet Dev , vol.16 , pp. 545-552
    • Bentley, D.1
  • 3
    • 3042666256 scopus 로고    scopus 로고
    • MUSCLE: Multiple sequence alignment with high accuracy and high throughput
    • Edgar, R. 2004. MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32, 1792-1797.
    • (2004) Nucleic Acids Res , vol.32 , pp. 1792-1797
    • Edgar, R.1
  • 4
    • 0031955518 scopus 로고    scopus 로고
    • Base-calling of automated sequencer traces using Phred. I. Accuracy assessment, genome research
    • Ewing, B., Hillier, L., Wendl, M., Green, P. 1998. Base-calling of automated sequencer traces using Phred. I. Accuracy assessment, genome research. Cold Spring Harbor Laboratory Press 8, 175-185.
    • (1998) Cold Spring Harbor Laboratory Press , vol.8 , pp. 175-185
    • Ewing, B.1    Hillier, L.2    Wendl, M.3    Green, P.4
  • 5
    • 0027649341 scopus 로고
    • Isoefficiency: Measuring the scalability of parallel algorithms and architectures
    • Grama, A., Gupta, A., Kumar, V. 1993. Isoefficiency: Measuring the scalability of parallel algorithms and architectures. IEEE parallel and Distributed Technology 1, 12-21.
    • (1993) IEEE Parallel and Distributed Technology , vol.1 , pp. 12-21
    • Grama, A.1    Gupta, A.2    Kumar, V.3
  • 6
    • 0030243005 scopus 로고    scopus 로고
    • A high-performance, portable implementation of the MPI message passing interface standard
    • Gropp, W., Lusk, E., Doss, N., Skjellum, A. 1996. A high-performance, portable implementation of the MPI message passing interface standard. Parallel Computing 22, 789-828.
    • (1996) Parallel Computing , vol.22 , pp. 789-828
    • Gropp, W.1    Lusk, E.2    Doss, N.3    Skjellum, A.4
  • 8
    • 0032849859 scopus 로고    scopus 로고
    • CAP3: A DNA sequence assembly program
    • Huang, X., Madan, A. 1999. CAP3: A DNA sequence assembly program. Genome Research 9, 868-877.
    • (1999) Genome Research , vol.9 , pp. 868-877
    • Huang, X.1    Madan, A.2
  • 11
    • 28844463698 scopus 로고    scopus 로고
    • Emerging technologies in DNA sequencing
    • Metzker, M. 2005. Emerging technologies in DNA sequencing. Genome Research 15, 1767-1776.
    • (2005) Genome Research , vol.15 , pp. 1767-1776
    • Metzker, M.1
  • 13
    • 0348091086 scopus 로고
    • De Bruijn sequences - A model example of the interaction of discrete mathematics and computer science
    • Ralston, A. 1982. De Bruijn sequences - A model example of the interaction of discrete mathematics and computer science. Math Mag 55, 131-143.
    • (1982) Math Mag , vol.55 , pp. 131-143
    • Ralston, A.1
  • 14
    • 0026743736 scopus 로고
    • Expected parallel time and sequential space complexity of graph and digraph problems
    • Reif, J., Spirakis, P. 1992. Expected parallel time and sequential space complexity of graph and digraph problems. Algorithmica 7, 597-630.
    • (1992) Algorithmica , vol.7 , pp. 597-630
    • Reif, J.1    Spirakis, P.2
  • 18
    • 0019887799 scopus 로고
    • Identification of common molecular subsequences
    • Smith, T., Waterman, M. 1981. Identification of common molecular subsequences. Journal of Molecular Biology 147, 195-197.
    • (1981) Journal of Molecular Biology , vol.147 , pp. 195-197
    • Smith, T.1    Waterman, M.2
  • 19
    • 0016700864 scopus 로고
    • Detection of specific sequences among DNA fragments Sseparated by gel electrophoresis
    • Southern, E. 1975. Detection of specific sequences among DNA fragments Sseparated by gel electrophoresis. Journal of Molecular Biology 98, 503-517.
    • (1975) Journal of Molecular Biology , vol.98 , pp. 503-517
    • Southern, E.1
  • 20
    • 0038497542 scopus 로고
    • Molecular structure of nucleic acids: A structure for deoxyribose nucleic acid
    • Watson, J., Crick, F. 1953. Molecular structure of nucleic acids: A structure for deoxyribose nucleic acid. Nature 171, 737-738.
    • (1953) Nature , vol.171 , pp. 737-738
    • Watson, J.1    Crick, F.2
  • 21
    • 45549101719 scopus 로고    scopus 로고
    • A new pheromone trail-based genetic algorithm for comparative genome assembly
    • Zhao, F., Zhao, F., Li, T., Bryant, D. A. 2008. A new pheromone trail-based genetic algorithm for comparative genome assembly. Nucleic Acids Res 36, 3455-3462.
    • (2008) Nucleic Acids Res , vol.36 , pp. 3455-3462
    • Zhao, F.1    Zhao, F.2    Li, T.3    Bryant, D.A.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.