메뉴 건너뛰기




Volumn 9, Issue 3, 1998, Pages 283-294

Parallel computation in biological sequence analysis

Author keywords

Algorithm; Alignment; Comparison; Computation; Database; Parallel; Retrieval; Search; Sequence; Speculative

Indexed keywords

BIBLIOGRAPHIC RETRIEVAL SYSTEMS; BIOLOGY; COMPUTER WORKSTATIONS; DISTRIBUTED DATABASE SYSTEMS; INFORMATION RETRIEVAL; NATURAL SCIENCES COMPUTING; PARALLEL ALGORITHMS; QUERY LANGUAGES; WIDE AREA NETWORKS;

EID: 0032024312     PISSN: 10459219     EISSN: None     Source Type: Journal    
DOI: 10.1109/71.674320     Document Type: Article
Times cited : (55)

References (54)
  • 1
    • 0026562263 scopus 로고
    • The SWISS-PROT Protein Sequence Data Bank
    • A. Bairoch and B. Boeckmann, "The SWISS-PROT Protein Sequence Data Bank," Nucleic Acids Research, vol. 20, pp. 2,019-2,022, 1992.
    • (1992) Nucleic Acids Research , vol.20
    • Bairoch, A.1    Boeckmann, B.2
  • 2
    • 0023518540 scopus 로고
    • A Strategy for the Rapid Multiple Alignment of Protein Sequences
    • G.J. Barton and M.J.E. Sternberg, "A Strategy for the Rapid Multiple Alignment of Protein Sequences," J. Molecular Biology, vol. 198, pp. 327-337, 1987.
    • (1987) J. Molecular Biology , vol.198 , pp. 327-337
    • Barton, G.J.1    Sternberg, M.J.E.2
  • 3
    • 0025303764 scopus 로고
    • Protein Multiple Sequence Alignment and Flexible Pattern Matching
    • G.J. Barton, "Protein Multiple Sequence Alignment and Flexible Pattern Matching," Methods in Enzymology, vol. 183, pp. 403-427, 1990.
    • (1990) Methods in Enzymology , vol.183 , pp. 403-427
    • Barton, G.J.1
  • 4
    • 0026069103 scopus 로고
    • Scanning Protein Sequence Databanks Using a Distributed Processing Workstation Network
    • G.J. Barton, "Scanning Protein Sequence Databanks Using a Distributed Processing Workstation Network," Computer Applications in the Biosciences, vol. 7, pp. 85-88, 1991.
    • (1991) Computer Applications in the Biosciences , vol.7 , pp. 85-88
    • Barton, G.J.1
  • 6
    • 0026009526 scopus 로고
    • A Novel Randomized Iteration Strategy for Aligning Multiple Protein Sequences
    • M.P. Berger and P.J. Munson, "A Novel Randomized Iteration Strategy for Aligning Multiple Protein Sequences," Computer Applications in the Biosciences, vol. 7, pp. 479-484, 1991.
    • (1991) Computer Applications in the Biosciences , vol.7 , pp. 479-484
    • Berger, M.P.1    Munson, P.J.2
  • 8
    • 0000262677 scopus 로고
    • BLAZE: An Implementation of the Smith-Waterman Sequence Comparison Algorithm on a Massively Parallel Computer
    • D.L. Brutlag, J.P. Dautricourt, R. Diaz, F. Fier, B. Moxon, and R. Stamm, "BLAZE: An Implementation of the Smith-Waterman Sequence Comparison Algorithm on a Massively Parallel Computer," Computers Chem., vol. 17, pp. 203-207, 1993.
    • (1993) Computers Chem. , vol.17 , pp. 203-207
    • Brutlag, D.L.1    Dautricourt, J.P.2    Diaz, R.3    Fier, F.4    Moxon, B.5    Stamm, R.6
  • 10
    • 0004531554 scopus 로고
    • OTA-BA-373, Washington, D.C., Government Printing Office, Apr.
    • U.S. Congress Office of Technology Assessment, "Mapping Our Genes - The Genome Projects: How Big, How Fast?" OTA-BA-373, Washington, D.C., Government Printing Office, Apr. 1988.
    • (1988) Mapping Our Genes - The Genome Projects: How Big, How Fast?
  • 11
    • 0024297354 scopus 로고
    • Multiple Sequence Alignment with Hierarchical Clustering
    • F. Corpet, "Multiple Sequence Alignment with Hierarchical Clustering," Nucleic Acids Research, vol. 16, no. 22, pp. 10,881-10,891, 1988.
    • (1988) Nucleic Acids Research , vol.16 , Issue.22
    • Corpet, F.1
  • 13
    • 0010136544 scopus 로고
    • The Human Genome Project
    • C. DeLisi, "The Human Genome Project," American Scientist, vol. 76, pp. 488-493, 1988.
    • (1988) American Scientist , vol.76 , pp. 488-493
    • DeLisi, C.1
  • 15
    • 33748260425 scopus 로고    scopus 로고
    • DNA Data Bank of Japan Nat'l Inst. of Genetics, Yata, Mishima, 411, Japan
    • DNA Data Bank of Japan Nat'l Inst. of Genetics, Yata, Mishima, 411, Japan, ftp address: ddbj@ddbj.nig.ac.jp.
  • 17
    • 33748279875 scopus 로고    scopus 로고
    • European Molecular Biology Laboratory, Postfach 10.2209, D-6900 Heidelberg, Federal Republic of Germany, E-mail: DataLib@EMBL-Heidelberg.DE
    • European Molecular Biology Laboratory, Postfach 10.2209, D-6900 Heidelberg, Federal Republic of Germany, E-mail: DataLib@EMBL-Heidelberg.DE.
  • 18
    • 0025025261 scopus 로고
    • Progressive Alignment and Phylogenetic Tree Construction of Protein Sequences
    • D.F. Feng and R.F. Doolittle, "Progressive Alignment and Phylogenetic Tree Construction of Protein Sequences," Methods in Enzymology, vol. 183, pp. 375-387, 1990.
    • (1990) Methods in Enzymology , vol.183 , pp. 375-387
    • Feng, D.F.1    Doolittle, R.F.2
  • 21
    • 0020484488 scopus 로고
    • An Improved Algorithm for Matching Biological Sequences
    • O. Gotoh, "An Improved Algorithm for Matching Biological Sequences," J. Molecular Biology, vol. 162, pp. 705-708, 1982.
    • (1982) J. Molecular Biology , vol.162 , pp. 705-708
    • Gotoh, O.1
  • 23
    • 0024234855 scopus 로고
    • CLUSTAL: A Package for Performing Multiple Sequence Alignment on a Microcomputer
    • D.G. Higgins and P.M. Sharp, "CLUSTAL: A Package for Performing Multiple Sequence Alignment on a Microcomputer," Gene, vol. 73, pp. 237-244, 1988.
    • (1988) Gene , vol.73 , pp. 237-244
    • Higgins, D.G.1    Sharp, P.M.2
  • 24
    • 0024598146 scopus 로고
    • Fast and Sensitive Multiple Sequence Alignments on a Microcomputer
    • D.G. Higgins and P.M. Sharp, "Fast and Sensitive Multiple Sequence Alignments on a Microcomputer," Computer Applications in the Biosciences, vol. 5, pp. 151-153, 1989.
    • (1989) Computer Applications in the Biosciences , vol.5 , pp. 151-153
    • Higgins, D.G.1    Sharp, P.M.2
  • 26
    • 0016518550 scopus 로고
    • A Linear Space Algorithm for Computing Maximal Common Subsequences
    • D.S. Hirschberg, "A Linear Space Algorithm for Computing Maximal Common Subsequences," Comm. ACM, vol. 18, pp. 341-343, 1975.
    • (1975) Comm. ACM , vol.18 , pp. 341-343
    • Hirschberg, D.S.1
  • 31
    • 0011769782 scopus 로고
    • Access to Molecular Biology Databases
    • To obtain the LiMB file, send the message: limb-data to bioserve@t10.Lanl.GOV
    • G. Keen, G. Redgrave, J. Lawton, M. Cinkowsky, S. Mishra, J. Fickett, and C. Burks, "Access to Molecular Biology Databases," Mathematical Computer Modeling, vol. 16, pp. 93-101, 1992. Internet: limb@life.lanl.gov. To obtain the LiMB file, send the message: limb-data to bioserve@t10.Lanl.GOV.
    • (1992) Mathematical Computer Modeling , vol.16 , pp. 93-101
    • Keen, G.1    Redgrave, G.2    Lawton, J.3    Cinkowsky, M.4    Mishra, S.5    Fickett, J.6    Burks, C.7
  • 33
    • 0001002027 scopus 로고
    • An Overview of Sequence Comparison: Time Warps, String Edits, and Macromolecules
    • J.B. Kruskal, "An Overview of Sequence Comparison: Time Warps, String Edits, and Macromolecules," SIAM Review, vol. 25, pp. 201-237, 1983.
    • (1983) SIAM Review , vol.25 , pp. 201-237
    • Kruskal, J.B.1
  • 34
    • 0343079052 scopus 로고
    • Study of Protein Sequence Comparison Metrics on the Connection Machine CM-2
    • E. Lander, J.P. Mesirov, and W. Taylor IV, "Study of Protein Sequence Comparison Metrics on the Connection Machine CM-2," J. Supercomputing, vol. 3, pp. 255-269, 1989.
    • (1989) J. Supercomputing , vol.3 , pp. 255-269
    • Lander, E.1    Mesirov, J.P.2    Taylor IV, W.3
  • 35
    • 0027912333 scopus 로고
    • Detecting Subtle Sequence Signals: A Gibbs Sampling Strategy for Multiple Alignment
    • C.L. Lawrence, S.F. Altschul, M.S. Boguski, J.S. Liu, A.F. Neuwald, and J.C. Wootton, "Detecting Subtle Sequence Signals: A Gibbs Sampling Strategy for Multiple Alignment," Science, vol. 262, pp. 208-214, 1993.
    • (1993) Science , vol.262 , pp. 208-214
    • Lawrence, C.L.1    Altschul, S.F.2    Boguski, M.S.3    Liu, J.S.4    Neuwald, A.F.5    Wootton, J.C.6
  • 36
    • 0024284078 scopus 로고
    • A Flexible Multiple Sequence Alignment Program
    • H.M. Martinez, "A Flexible Multiple Sequence Alignment Program," Nucleic Acids Research, vol. 16, pp. 1,683-1,691, 1988.
    • (1988) Nucleic Acids Research , vol.16
    • Martinez, H.M.1
  • 37
    • 0026538781 scopus 로고
    • Comparing Machine-Independent versus Machine-Specific Parallelization of a Software Platform for Biological Sequence Comparison
    • P.L. Miller, P.M. Nadkarni, and W.R. Pearson, "Comparing Machine-Independent versus Machine-Specific Parallelization of a Software Platform for Biological Sequence Comparison," Computer Applications in the Biosciences, vol. 8, pp. 167-175, 1992.
    • (1992) Computer Applications in the Biosciences , vol.8 , pp. 167-175
    • Miller, P.L.1    Nadkarni, P.M.2    Pearson, W.R.3
  • 39
    • 0025275576 scopus 로고
    • Three-Way Needleman-Wunsch Algorithm
    • M. Murata, "Three-Way Needleman-Wunsch Algorithm," Methods in Enzymology, vol. 183, pp. 365-375, 1990.
    • (1990) Methods in Enzymology , vol.183 , pp. 365-375
    • Murata, M.1
  • 41
    • 0014757386 scopus 로고
    • A General Method Applicable to the Search for Similarities in the Amino Acid Sequence of Two Sequences
    • S.B. Needleman and C.D. Wunsch, "A General Method Applicable to the Search for Similarities in the Amino Acid Sequence of Two Sequences," J. Molecular Biology, vol. 48, pp. 443-453, 1970.
    • (1970) J. Molecular Biology , vol.48 , pp. 443-453
    • Needleman, S.B.1    Wunsch, C.D.2
  • 42
    • 33748258542 scopus 로고    scopus 로고
    • Protein Information Resource Nat'l Biomedical Research Foundation, 3900 Reservoir Road, N.W., Washington, D.C. 20007, E-mail: PIRMAIL@GUNBRF.bitnet
    • Protein Information Resource Nat'l Biomedical Research Foundation, 3900 Reservoir Road, N.W., Washington, D.C. 20007, E-mail: PIRMAIL@GUNBRF.bitnet.
  • 43
    • 0025905073 scopus 로고
    • A Parallel Computing Approach to Genetic Sequence Comparison: The Master-Worker Paradigm with Interworker Communication
    • D.F. Sittig, D. Foulser, N. Carriero, G. McCorkle, and P.L. Miller, "A Parallel Computing Approach to Genetic Sequence Comparison: The Master-Worker Paradigm with Interworker Communication," Computers and Biomedical Research, vol. 24, pp. 152-169, 1991.
    • (1991) Computers and Biomedical Research , vol.24 , pp. 152-169
    • Sittig, D.F.1    Foulser, D.2    Carriero, N.3    McCorkle, G.4    Miller, P.L.5
  • 44
    • 0019887799 scopus 로고
    • Identification of Common Molecular Subsequence
    • T.F. Smith and M.S. Waterman, "Identification of Common Molecular Subsequence," J. Molecular Biology, vol. 147, pp. 195-197, 1981.
    • (1981) J. Molecular Biology , vol.147 , pp. 195-197
    • Smith, T.F.1    Waterman, M.S.2
  • 45
    • 0029386329 scopus 로고
    • Parallel N-ary Speculative Computation of Simulated Annealing
    • A. Sohn, "Parallel N-ary Speculative Computation of Simulated Annealing," IEEE Trans. Parallel and Distributed Systems, vol. 6, pp. 997-1005, 1995.
    • (1995) IEEE Trans. Parallel and Distributed Systems , vol.6 , pp. 997-1005
    • Sohn, A.1
  • 46
    • 0023364009 scopus 로고
    • Multiple Sequence Alignment by a Pairwise Algorithm
    • W.R. Taylor, "Multiple Sequence Alignment by a Pairwise Algorithm," Computer Applications in the Biosciences, vol. 3, pp. 81-87, 1987.
    • (1987) Computer Applications in the Biosciences , vol.3 , pp. 81-87
    • Taylor, W.R.1
  • 47
    • 0024245156 scopus 로고
    • A Flexible Method to Align Large Numbers of Biological Sequences
    • W.R. Taylor, "A Flexible Method to Align Large Numbers of Biological Sequences," J. Molecular Evolution, vol. 28, pp. 161-169, 1988.
    • (1988) J. Molecular Evolution , vol.28 , pp. 161-169
    • Taylor, W.R.1
  • 48
    • 0027070512 scopus 로고
    • Spectral and Sequence Similarity between Vasoactive Intestinal Peptide and the Second Conserved Region of Human Immunodeficiency Virus Type 1 Envelope Glycoprotein (gp120): Possible Consequences on Prevention and Therapy of AIDS
    • V. Veljkovic, R. Meltlas, J. Raspopovic, and S. Pongor, "Spectral and Sequence Similarity between Vasoactive Intestinal Peptide and the Second Conserved Region of Human Immunodeficiency Virus Type 1 Envelope Glycoprotein (gp120): Possible Consequences on Prevention and Therapy of AIDS," Biochemical and Biophysical Research Comm., vol. 189, pp. 705-710, 1992.
    • (1992) Biochemical and Biophysical Research Comm. , vol.189 , pp. 705-710
    • Veljkovic, V.1    Meltlas, R.2    Raspopovic, J.3    Pongor, S.4
  • 49
    • 0028074616 scopus 로고
    • Isolation of Differentially Expressed Sequence Tags from Human Breast Cancer
    • M.A. Watson and T.P. Fleming, "Isolation of Differentially Expressed Sequence Tags from Human Breast Cancer," Cancer Research, vol. 54, pp. 4,598-4,602, 1994.
    • (1994) Cancer Research , vol.54
    • Watson, M.A.1    Fleming, T.P.2
  • 51
    • 33748274751 scopus 로고    scopus 로고
    • Parallel Computation in Biomedicine: Genetic and Protein Sequence Analysis
    • A.Y. Zomaya, ed., McGraw-Hill
    • T.K. Yap, O. Frieder, and R.L. Martino, "Parallel Computation in Biomedicine: Genetic and Protein Sequence Analysis," Handbook of Parallel and Distributing Computing, A.Y. Zomaya, ed., pp. 1,071-1,096. McGraw-Hill, 1996.
    • (1996) Handbook of Parallel and Distributing Computing
    • Yap, T.K.1    Frieder, O.2    Martino, R.L.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.