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Volumn 1, Issue 3, 2004, Pages 116-129

Improved gapped alignment in BLAST

Author keywords

BLAST; Dynamic programming; Homology search; Sequence alignment

Indexed keywords

ALGORITHMS; COMPUTATIONAL METHODS; GENES; HEURISTIC METHODS; OPTIMIZATION; SERVERS; WEBSITES;

EID: 14744270579     PISSN: 15455963     EISSN: None     Source Type: Journal    
DOI: 10.1109/TCBB.2004.32     Document Type: Article
Times cited : (84)

References (37)
  • 1
    • 0028289467 scopus 로고
    • Issues in searching molecular sequence databases
    • S. Altschul, M. Boguski, W. Gish, and J. Wootton, "Issues in Searching Molecular Sequence Databases," Nature Genetics, vol. 6, pp. 119-129, 1994
    • (1994) Nature Genetics , vol.6 , pp. 119-129
    • Altschul, S.1    Boguski, M.2    Gish, W.3    Wootton, J.4
  • 2
    • 0032126517 scopus 로고    scopus 로고
    • Generalized affine gap costs for protein sequence alignment
    • S.F. Altschul, "Generalized Affine Gap Costs for Protein Sequence Alignment," PROTEINS: Structure, Function, and Genetics, vol. 32, no. 1, pp. 88-96, 1998.
    • (1998) PROTEINS: Structure, Function, and Genetics , vol.32 , Issue.1 , pp. 88-96
    • Altschul, S.F.1
  • 3
    • 0035863762 scopus 로고    scopus 로고
    • The estimation of statistical parameters for local alignment score distributions
    • S.F. Altschul, R. Bundschuh, R. Olsen, and T. Hwa, "The Estimation of Statistical Parameters for Local Alignment Score Distributions," Nucleic Acids Research, vol. 29, no. 2, pp. 351-361, 2001.
    • (2001) Nucleic Acids Research , vol.29 , Issue.2 , pp. 351-361
    • Altschul, S.F.1    Bundschuh, R.2    Olsen, R.3    Hwa, T.4
  • 4
    • 0029889221 scopus 로고    scopus 로고
    • Local alignment statistics
    • S.F. Altschul and W. Gish, "Local Alignment Statistics," Methods in Enzymology, vol. 266, pp. 460-480, 1996.
    • (1996) Methods in Enzymology , vol.266 , pp. 460-480
    • Altschul, S.F.1    Gish, W.2
  • 9
    • 0032568596 scopus 로고    scopus 로고
    • Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships
    • S.E. Brenner, C. Chothia, and T.J.P. Hubbard, "Assessing Sequence Comparison Methods with Reliable Structurally Identified Distant Evolutionary Relationships," Proc. Nat'l Academy of Sciences USA, vol. 95, no. 11, pp. 6073-6078, 1998.
    • (1998) Proc. Nat'l Academy of Sciences USA , vol.95 , Issue.11 , pp. 6073-6078
    • Brenner, S.E.1    Chothia, C.2    Hubbard, T.J.P.3
  • 11
    • 0028679375 scopus 로고
    • Recent developments in linear-space alignment methods: A survey
    • K.M. Chao, R.C. Hardison, and W. Miller, "Recent Developments in Linear-Space Alignment Methods: A Survey," J. Computational Biology, vol. 1, no. 4, pp. 271-91, 1994.
    • (1994) J. Computational Biology , vol.1 , Issue.4 , pp. 271-291
    • Chao, K.M.1    Hardison, R.C.2    Miller, W.3
  • 13
    • 14744268051 scopus 로고    scopus 로고
    • personal comm.
    • X.L. Chen, personal comm., 2004.
    • (2004)
    • Chen, L.1
  • 14
    • 0346252359 scopus 로고    scopus 로고
    • Assessing sequence comparison methods with the average precision criterion
    • Z. Chen, "Assessing Sequence Comparison Methods with the Average Precision Criterion," Bioinformatics, vol. 19, no. 18, pp. 2456-2460, 2003.
    • (2003) Bioinformatics , vol.19 , Issue.18 , pp. 2456-2460
    • Chen, Z.1
  • 17
    • 0020484488 scopus 로고
    • An improved algorithm for matching biological sequences
    • O. Gotoh, "An Improved Algorithm for Matching Biological Sequences," J. Molecular Biology, vol. 162, no. 3, pp. 705-708, 1982.
    • (1982) J. Molecular Biology , vol.162 , Issue.3 , pp. 705-708
    • Gotoh, O.1
  • 18
    • 0001969211 scopus 로고    scopus 로고
    • Use of receiver Operating Characteristic (ROC) analysis to evaluate sequence matching
    • M. Gribskov and N.L. Robinson, "Use of Receiver Operating Characteristic (ROC) Analysis to Evaluate Sequence Matching," Computers & Chemistry, vol. 20, pp. 25-33, 1996.
    • (1996) Computers & Chemistry , vol.20 , pp. 25-33
    • Gribskov, M.1    Robinson, N.L.2
  • 20
    • 0026458378 scopus 로고
    • Amino acid substitution matrices from protein blocks
    • S. Henikoff and J. Henikoff, "Amino Acid Substitution Matrices from Protein Blocks," Proc. Nat'l Academy of Sciences, vol. 89, no. 22, pp. 10915-10919, 1992.
    • (1992) Proc. Nat'l Academy of Sciences , vol.89 , Issue.22 , pp. 10915-10919
    • Henikoff, S.1    Henikoff, J.2
  • 21
    • 0025259313 scopus 로고
    • Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes
    • S. Karlin and S.F. Altschul, "Methods for Assessing the Statistical Significance of Molecular Sequence Features by Using General Scoring Schemes," Proc. Nat'l Academy of Sciences, vol. 87, no. 6, pp. 2264-2268, 1990.
    • (1990) Proc. Nat'l Academy of Sciences , vol.87 , Issue.6 , pp. 2264-2268
    • Karlin, S.1    Altschul, S.F.2
  • 22
    • 0036226603 scopus 로고    scopus 로고
    • BLAT-The BLAST-like alignment tool
    • W.J. Kent, "BLAT-The BLAST-Like Alignment Tool," Genome Research, vol. 12, no. 4, pp. 656-664, 2002.
    • (2002) Genome Research , vol.12 , Issue.4 , pp. 656-664
    • Kent, W.J.1
  • 24
    • 0036202921 scopus 로고    scopus 로고
    • Patternhunter: Faster and more sensitive homology search
    • B. Ma, J. Tromp, and M. Li, "Patternhunter: Faster and More Sensitive Homology Search," Bioinformatics, vol. 18, no. 3, pp. 440-445, 2002.
    • (2002) Bioinformatics , vol.18 , Issue.3 , pp. 440-445
    • Ma, B.1    Tromp, J.2    Li, M.3
  • 25
    • 3242876311 scopus 로고    scopus 로고
    • BLAST: At the core of a powerful and diverse set of sequence analysis tools
    • S. McGinnis and T.L. Madden, "BLAST: At the Core of a Powerful and Diverse Set of Sequence Analysis Tools," Nucleic Acids Research, vol. 32, pp. W20-W25, 2004.
    • (2004) Nucleic Acids Research , vol.32
    • McGinnis, S.1    Madden, T.L.2
  • 26
    • 0028961335 scopus 로고
    • SCOP: A structural classification of proteins database for the investigation of sequences and structures
    • A.G. Murzin, S.E. Brenner, T. Hubbard, and C. Chothia, "SCOP: A Structural Classification of Proteins Database for the Investigation of Sequences and Structures," J. Molecular Biology, vol. 247, no. 4, pp. 536-540, 1995.
    • (1995) J. Molecular Biology , vol.247 , Issue.4 , pp. 536-540
    • Murzin, A.G.1    Brenner, S.E.2    Hubbard, T.3    Chothia, C.4
  • 28
    • 0038020939 scopus 로고    scopus 로고
    • A table-driven, full-sensitivity similarity search algorithm
    • G. Myers and R. Durbin, "A Table-Driven, Full-Sensitivity Similarity Search Algorithm," J. Computational Biology, vol. 10, no. 2, pp. 103-117, 2003.
    • (2003) J. Computational Biology , vol.10 , Issue.2 , pp. 103-117
    • Myers, G.1    Durbin, R.2
  • 29
    • 0032509105 scopus 로고    scopus 로고
    • Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods
    • J. Park, K. Karplus, C. Barrett, R. Hughey, D. Haussler, T. Hubbard, and C. Chothia, "Sequence Comparisons Using Multiple Sequences Detect Three Times as Many Remote Homologues as Pairwise Methods," J. Molecular Biology, vol. 284, no. 4, pp. 1201-1210, 1998.
    • (1998) J. Molecular Biology , vol.284 , Issue.4 , pp. 1201-1210
    • Park, J.1    Karplus, K.2    Barrett, C.3    Hughey, R.4    Haussler, D.5    Hubbard, T.6    Chothia, C.7
  • 30
    • 0021919480 scopus 로고
    • Rapid and sensitive protein similarity searches
    • W.R. Pearson and D.J. Lipman, "Rapid and Sensitive Protein Similarity Searches," Science, vol. 227, no. 4693, pp. 1435-1441, 1985.
    • (1985) Science , vol.227 , Issue.4693 , pp. 1435-1441
    • Pearson, W.R.1    Lipman, D.J.2
  • 31
    • 0023989064 scopus 로고
    • Improved tools for biological sequence comparison
    • W.R. Pearson and D.J. Lipman, "Improved Tools for Biological Sequence Comparison," Proc. Nat'l Academy of Sciences, vol. 85, no. 8, pp. 2444-2448, 1988.
    • (1988) Proc. Nat'l Academy of Sciences , vol.85 , Issue.8 , pp. 2444-2448
    • Pearson, W.R.1    Lipman, D.J.2
  • 32
    • 0026651391 scopus 로고
    • Dynamic programming algorithms for biological sequence comparison
    • W.R. Pearson and W. Miller, "Dynamic Programming Algorithms for Biological Sequence Comparison," Methods in Enzymology, vol. 210, pp. 575-601, 1992.
    • (1992) Methods in Enzymology , vol.210 , pp. 575-601
    • Pearson, W.R.1    Miller, W.2
  • 33
  • 34
    • 0019887799 scopus 로고
    • Identification of common molecular subsequences
    • T.F. Smith and M.S. Waterman, "Identification of Common Molecular Subsequences," J. Molecular Biology, vol. 147, no. 1, pp. 195-197, 1981.
    • (1981) J. Molecular Biology , vol.147 , Issue.1 , pp. 195-197
    • Smith, T.F.1    Waterman, M.S.2
  • 35
    • 0020714456 scopus 로고
    • Rapid similarity searches of nucleic acid and protein data banks
    • W.J. Wilbur and D.J. Lipman, "Rapid Similarity Searches of Nucleic Acid and Protein Data Banks," Proc. Nat'l Academy of Sciences, vol. 80, no. 3, pp. 726-730, 1983.
    • (1983) Proc. Nat'l Academy of Sciences , vol.80 , Issue.3 , pp. 726-730
    • Wilbur, W.J.1    Lipman, D.J.2
  • 36
    • 0031927028 scopus 로고    scopus 로고
    • Alignments without low-scoring regions
    • Z. Zhang, P. Berman, and W. Miller, "Alignments without Low-Scoring Regions," J. Computational Biology, vol. 5, no. 2, pp. 197-210, 1998.
    • (1998) J. Computational Biology , vol.5 , Issue.2 , pp. 197-210
    • Zhang, Z.1    Berman, P.2    Miller, W.3
  • 37
    • 0030790426 scopus 로고    scopus 로고
    • Aligning a DNA sequence with a protein sequence
    • Z. Zhang, W. Pearson, and W. Miller, "Aligning a DNA Sequence with a Protein Sequence," J. Computational Biology, vol. 4, no. 3, pp. 339-349, 1997.
    • (1997) J. Computational Biology , vol.4 , Issue.3 , pp. 339-349
    • Zhang, Z.1    Pearson, W.2    Miller, W.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.