메뉴 건너뛰기




Volumn 1, Issue , 2008, Pages 40-66

Statistical Significance in Biological Sequence Comparison

Author keywords

Accepted point mutation; Aligned amino acid residues; Archebacterial genome; Caenorhabditis elegans; E. coli transcription termination factor; Membrane spanning protein; Molecular homology; Prokaryotic and eukaryotic proteins; Randomly shuffled human histone; Unrelated and low complexity sequences

Indexed keywords


EID: 84879418896     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/9780470061619.ch2     Document Type: Chapter
Times cited : (13)

References (50)
  • 2
    • 0025878149 scopus 로고
    • Amino acid substitution matrices from an information theoretic perspective
    • Altschul, S.F. (1991). Amino acid substitution matrices from an information theoretic perspective. Journal of Molecular Biology 219, 555-565.
    • (1991) Journal of Molecular Biology , vol.219 , pp. 555-565
    • Altschul, S.F.1
  • 8
    • 0000960430 scopus 로고
    • The Erdös-Rényi law in distribution, for coin tossing and sequence matching
    • Arratia, R., Gordon, L. and Waterman, M.S. (1990). The Erdös-Rényi law in distribution, for coin tossing and sequence matching. Annals of Statistics 18, 539-570.
    • (1990) Annals of Statistics , vol.18 , pp. 539-570
    • Arratia, R.1    Gordon, L.2    Waterman, M.S.3
  • 9
    • 0029916911 scopus 로고    scopus 로고
    • The Swiss-Prot protein sequence data bank and its new supplement TrEMBL
    • Bairoch, A. and Apweiler, R. (1996). The Swiss-Prot protein sequence data bank and its new supplement TrEMBL. Nucleic Acids Research 24, 21-25.
    • (1996) Nucleic Acids Research , vol.24 , pp. 21-25
    • Bairoch, A.1    Apweiler, R.2
  • 10
    • 0030983386 scopus 로고    scopus 로고
    • Population statistics of protein structures: lessons from structural classifications
    • Brenner, S.E., Chothia, C. and Hubbard, T.J. (1997). Population statistics of protein structures: lessons from structural classifications. Current Opinion in Structural Biology 7, 369-376.
    • (1997) Current Opinion in Structural Biology , vol.7 , pp. 369-376
    • Brenner, S.E.1    Chothia, C.2    Hubbard, T.J.3
  • 11
    • 0032568596 scopus 로고    scopus 로고
    • Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships
    • Brenner, S.E., Chothia, C. and Hubbard, T.J. (1998). Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships. Proceedings of the National Academy of Sciences (USA) 95, 6073-6078.
    • (1998) Proceedings of the National Academy of Sciences (USA) , vol.95 , pp. 6073-6078
    • Brenner, S.E.1    Chothia, C.2    Hubbard, T.J.3
  • 14
    • 0000228203 scopus 로고
    • Atlas of Protein Sequence and Structure
    • M. Dayhoff, ed. National Biomedical Research Foundation, Silver Spring, MD
    • Dayhoff, M., Schwartz, R.M. and Orcutt, B.C. (1978). In Atlas of Protein Sequence and Structure, Vol. 5, supplement 3, M. Dayhoff, ed. National Biomedical Research Foundation, Silver Spring, MD, pp. 345-352.
    • (1978) , vol.5 , Issue.SUPPL. 3 , pp. 345-352
    • Dayhoff, M.1    Schwartz, R.M.2    Orcutt, B.C.3
  • 15
    • 0027983037 scopus 로고
    • Convergent evolution: the need to be explicit
    • Doolittle, R.F. (1994). Convergent evolution: the need to be explicit. Trends in Biochemical Sciences 19, 15-18.
    • (1994) Trends in Biochemical Sciences , vol.19 , pp. 15-18
    • Doolittle, R.F.1
  • 16
    • 0004083354 scopus 로고
    • Statistical Distributions
    • 2nd edition. Wiley, New York
    • Evans, M., Hastings, N. and Peacock, B. (1993). Statistical Distributions, 2nd edition. Wiley, New York.
    • (1993)
    • Evans, M.1    Hastings, N.2    Peacock, B.3
  • 17
    • 0013889249 scopus 로고
    • An improved method of testing for evolutionary homology
    • Fitch, W.M. (1966). An improved method of testing for evolutionary homology. Journal of Molecular Biology 16, 9-16.
    • (1966) Journal of Molecular Biology , vol.16 , pp. 9-16
    • Fitch, W.M.1
  • 21
    • 0001079105 scopus 로고
    • On the use of sequence homologies to predict protein structure: identical pentapeptides can have completely different conformations
    • Kabsch, W. and Sander, C. (1984). On the use of sequence homologies to predict protein structure: identical pentapeptides can have completely different conformations. Proceedings of the National Academy of Sciences (USA) 81, 1075-1078.
    • (1984) Proceedings of the National Academy of Sciences (USA) , vol.81 , pp. 1075-1078
    • Kabsch, W.1    Sander, C.2
  • 22
    • 0025259313 scopus 로고
    • Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes
    • Karlin, S. and Altschul, S.F. (1990). Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes. Proceedings of the National Academy of Sciences (USA) 87, 2264-2268.
    • (1990) Proceedings of the National Academy of Sciences (USA) , vol.87 , pp. 2264-2268
    • Karlin, S.1    Altschul, S.F.2
  • 24
    • 0003847586 scopus 로고
    • Comparative Anatomy of the Vertebrates
    • Mosby, St. Louis, MO
    • Kent, G.C. (1992). Comparative Anatomy of the Vertebrates. Mosby, St. Louis, MO.
    • (1992)
    • Kent, G.C.1
  • 25
    • 0030907680 scopus 로고    scopus 로고
    • Big time for small genomes
    • Koonin, E.V. (1997). Big time for small genomes. Genome Research 7, 418-421.
    • (1997) Genome Research , vol.7 , pp. 418-421
    • Koonin, E.V.1
  • 26
    • 0020475449 scopus 로고
    • A simple method for displaying the hydropathic character of a protein
    • Kyte, J. and Doolittle, R.F. (1982). A simple method for displaying the hydropathic character of a protein. Journal of Molecular Biology 157, 105-132.
    • (1982) Journal of Molecular Biology , vol.157 , pp. 105-132
    • Kyte, J.1    Doolittle, R.F.2
  • 27
    • 0032568649 scopus 로고    scopus 로고
    • A unified statistical framework for sequence comparison and structure comparison
    • Levitt, M. and Gerstein, M. (1998). A unified statistical framework for sequence comparison and structure comparison. Proceedings of the National Academy of Sciences (USA) 95, 5913-5920.
    • (1998) Proceedings of the National Academy of Sciences (USA) , vol.95 , pp. 5913-5920
    • Levitt, M.1    Gerstein, M.2
  • 28
    • 0021919480 scopus 로고
    • Rapid and sensitive protein similarity searches
    • Lipman, D.J. and Pearson, W.R. (1985). Rapid and sensitive protein similarity searches. Science 227, 1435-1441.
    • (1985) Science , vol.227 , pp. 1435-1441
    • Lipman, D.J.1    Pearson, W.R.2
  • 29
    • 0002064379 scopus 로고
    • Maximum likelihood estimation of the statistical distribution of Smith-Waterman local sequence similarity scores
    • Mott, R. (1992). Maximum likelihood estimation of the statistical distribution of Smith-Waterman local sequence similarity scores. Bulletin of Mathematical Biology 54, 59-75.
    • (1992) Bulletin of Mathematical Biology , vol.54 , pp. 59-75
    • Mott, R.1
  • 30
    • 0014757386 scopus 로고
    • A general method applicable to the search for similarities in the amino acid sequences of two proteins
    • Needleman, S. and Wunsch, C. (1970). A general method applicable to the search for similarities in the amino acid sequences of two proteins. Journal of Molecular Biology 48, 444-453.
    • (1970) Journal of Molecular Biology , vol.48 , pp. 444-453
    • Needleman, S.1    Wunsch, C.2
  • 31
    • 0014220925 scopus 로고
    • Evolution of structure and function of proteases
    • Neurath, H., Walsh, K.A. and Winter, W.P. (1967). Evolution of structure and function of proteases. Science 158, 1638-1644.
    • (1967) Science , vol.158 , pp. 1638-1644
    • Neurath, H.1    Walsh, K.A.2    Winter, W.P.3
  • 32
    • 0028856715 scopus 로고
    • Structural similarity between the pleckstrin homology domain and verotoxin: the problem of measuring and evaluating structural similarity
    • Orengo, C.A., Swindells, M.B., Michie, A.D., Zvelebil, M.J., Driscoll, P.C., Waterfield, M.D. and Thornton, J.M. (1995). Structural similarity between the pleckstrin homology domain and verotoxin: the problem of measuring and evaluating structural similarity. Protein Science 4, 1977-1983.
    • (1995) Protein Science , vol.4 , pp. 1977-1983
    • Orengo, C.A.1    Swindells, M.B.2    Michie, A.D.3    Zvelebil, M.J.4    Driscoll, P.C.5    Waterfield, M.D.6    Thornton, J.M.7
  • 33
    • 0003568052 scopus 로고
    • Lectures on the Comparative Anatomy and Physiology of the Invertebrate Animals
    • Longman, Brown, Green and Co., London
    • Owen, R. (1843). Lectures on the Comparative Anatomy and Physiology of the Invertebrate Animals. Longman, Brown, Green and Co., London.
    • (1843)
    • Owen, R.1
  • 34
    • 0004079284 scopus 로고
    • On the Anatomy of Vertebrates
    • Longmans, Green and Co., London
    • Owen, R. (1866). On the Anatomy of Vertebrates. Longmans, Green and Co., London.
    • (1866)
    • Owen, R.1
  • 35
    • 0029006770 scopus 로고
    • Comparison of methods for searching protein sequence databases
    • Pearson, W.R. (1995). Comparison of methods for searching protein sequence databases. Protein Science 4, 1145-1160.
    • (1995) Protein Science , vol.4 , pp. 1145-1160
    • Pearson, W.R.1
  • 36
    • 0029933671 scopus 로고    scopus 로고
    • Effective protein sequence comparison
    • Pearson, W.R. (1996). Effective protein sequence comparison. Methods in Enzymology 266, 227-258.
    • (1996) Methods in Enzymology , vol.266 , pp. 227-258
    • Pearson, W.R.1
  • 37
  • 38
    • 0032512799 scopus 로고    scopus 로고
    • Empirical statistical estimates for sequence similarity searches
    • Pearson, W.R. (1998). Empirical statistical estimates for sequence similarity searches. Journal of Molecular Biology 276, 71-84.
    • (1998) Journal of Molecular Biology , vol.276 , pp. 71-84
    • Pearson, W.R.1
  • 39
    • 0000154232 scopus 로고    scopus 로고
    • BioinformaticsMethods and Protocols
    • S. Misener and S.A. Krawetz, eds. Humana Press, Totowa, NJ
    • Pearson, W.R. (1999). In BioinformaticsMethods and Protocols, S. Misener and S.A. Krawetz, eds. Humana Press, Totowa, NJ, pp. 185-219.
    • (1999) , pp. 185-219
    • Pearson, W.R.1
  • 40
    • 0027479821 scopus 로고
    • Evolutionary families of peptidases
    • Rawlings, N.D. and Barrett, A. (1993). Evolutionary families of peptidases. Biochemical Journal 290, 205-218.
    • (1993) Biochemical Journal , vol.290 , pp. 205-218
    • Rawlings, N.D.1    Barrett, A.2
  • 41
    • 0003697181 scopus 로고    scopus 로고
    • Homoplasy: The Recurrence of Similarity in Evolution
    • Academic Press, New York
    • Sanderson, M. and Hufford, L. (eds) (1996). Homoplasy: The Recurrence of Similarity in Evolution. Academic Press, New York.
    • (1996)
    • Sanderson, M.1    Hufford, L.2
  • 42
    • 0000228203 scopus 로고
    • Atlas of Protein Sequence and Structure
    • M. Dayhoff, ed. National Biomedical Research Foundation, Silver Spring, MD
    • Schwartz, R.M. and Dayhoff, M. (1978). In Atlas of Protein Sequence and Structure, Vol. 5, supplement 3, M. Dayhoff, ed. National Biomedical Research Foundation, Silver Spring, MD, pp. 353-358.
    • (1978) , vol.5 , Issue.SUPPL. 3 , pp. 353-358
    • Schwartz, R.M.1    Dayhoff, M.2
  • 43
    • 0019887799 scopus 로고
    • Identification of common molecular subsequences
    • Smith, T.F. andWaterman, M.S. (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.F.1    Waterman, M.S.2
  • 44
    • 0030925920 scopus 로고    scopus 로고
    • Pfam: a comprehensive database of protein domain families based on seed alignments
    • Sonnhammer, E.L., Eddy, S.R. and Durbin, R. (1997). Pfam: a comprehensive database of protein domain families based on seed alignments. Proteins 28, 405-420.
    • (1997) Proteins , vol.28 , pp. 405-420
    • Sonnhammer, E.L.1    Eddy, S.R.2    Durbin, R.3
  • 45
    • 0002164370 scopus 로고
    • Improved sensitivity of nucleic acid database searches using application-specific scoring matrices
    • States, D.J., Gish, W. and Altschul, S.F. (1991). Improved sensitivity of nucleic acid database searches using application-specific scoring matrices. METHODS: A Companion to Methods in Enzymology 3, 66-70.
    • (1991) METHODS: A Companion to Methods in Enzymology , vol.3 , pp. 66-70
    • States, D.J.1    Gish, W.2    Altschul, S.F.3
  • 46
    • 0003512471 scopus 로고
    • Introduction to Computational Biology
    • Chapman and Hall, London
    • Waterman, M.S. (1995). Introduction to Computational Biology. Chapman and Hall, London.
    • (1995)
    • Waterman, M.S.1
  • 47
    • 0023661088 scopus 로고
    • A new algorithm for best subsequences alignment with application to tRNA-rRNA comparisons
    • Waterman, M.S. and Eggert, M. (1987). A new algorithm for best subsequences alignment with application to tRNA-rRNA comparisons. Journal of Molecular Biology 197, 723-728.
    • (1987) Journal of Molecular Biology , vol.197 , pp. 723-728
    • Waterman, M.S.1    Eggert, M.2
  • 48
    • 0028234758 scopus 로고
    • Rapid and accurate estimates of the statistical significance for sequence database searches
    • Waterman, M.S. and Vingron, M. (1994). Rapid and accurate estimates of the statistical significance for sequence database searches. Proceedings of the National Academy of Sciences (USA) 91, 4625-4628.
    • (1994) Proceedings of the National Academy of Sciences (USA) , vol.91 , pp. 4625-4628
    • Waterman, M.S.1    Vingron, M.2
  • 49
    • 0000708185 scopus 로고
    • Comparison between the amino acid sequences of sperm whale myoglobin and of human haemoglobin
    • Watson, H.C. and Kendrew, J. (1961). Comparison between the amino acid sequences of sperm whale myoglobin and of human haemoglobin. Nature 190, 670-672.
    • (1961) Nature , vol.190 , pp. 670-672
    • Watson, H.C.1    Kendrew, J.2
  • 50
    • 0028501914 scopus 로고
    • Non-globular domains in protein sequences: automated segmentation using complexity measures
    • Wootton, J.C. (1994). Non-globular domains in protein sequences: automated segmentation using complexity measures. Computers and Chemistry 18, 269-285.
    • (1994) Computers and Chemistry , vol.18 , pp. 269-285
    • Wootton, J.C.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.