An assessment of substitution scores for protein profile-profile comparison

Bioinformatics

Volumn 27, Issue 24, 2011, Pages 3356-3363

  Ye, Xugang ^a   Wang, Guoli ^b   Altschul, Stephen F ^a  

^a NATIONAL INSTITUTES OF HEALTH   (United States)

^b NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; BIOLOGY; CHEMISTRY; EUKARYOTE; METHODOLOGY; PROBABILITY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS;

AMINO ACID SEQUENCE; COMPUTATIONAL BIOLOGY; EUKARYOTA; PROBABILITY; PROTEINS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN;

EID: 83355177252     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btr565     Document Type: Article

References (70)

1. Altschul, S.F. (1989) Gap costs for multiple sequence alignment. J. Theor. Biol., 138, 297-309.
2. Altschul, S.F. (1991) Amino acid substitution matrices from an information theoretic perspective. J. Mol. Biol., 219, 555-565.
3. Altschul, S.F. and Lipman, D.J. (1989) Trees, stars, and multiple biological sequence alignment. SIAM J. Appl. Math., 49, 197-209.
4. Altschul, S.F. et al. (1989)Weights for data related by a tree. J. Mol. Biol., 207, 647-653.
5. Altschul, S.F. et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
6. Altschul, S.F. et al. (2009) PSI-BLAST pseudocounts and the minimum description length principle. Nucleic Acids Res., 37, 815-824.
7. Altschul, S.F. et al. (2010) The construction and use of log-odds substitution scores for multiple sequence alignment. PLoS Comput. Biol., 6, e1000852.
8. Bacon, D.J. and Anderson, W.F. (1986) Multiple sequence alignment. J. Mol. Biol., 191, 153-161.
9. Bailey, T.L. and Gribskov, M. (1996) The megaprior heuristic for discovering protein sequence patterns. In States, D.J. et al. (eds) Proceedings of the Fourth Intenational Conference Intelligent Systems for Molecular Biology. AAAI Press, Menlo Park, CA, pp. 15-24.
10. Berger, M.P. and Munson, P.J. (1991) A novel randomized iterative strategy for aligning multiple protein sequences. Comput. Appl. Biosci., 7, 479-484.
11. Brown, M. et al. (1993) Using Dirichlet mixture priors to derive hidden Markov models for protein families. In Hunter, L. et al. (eds) Proceedings of the First International Conference Intelligent Systems for Molecular Biology. AAAI Press, Menlo Park, CA, pp. 47-55.
12. Brown, D.P. et al. (1997) Automated protein subfamily identification and classification. PLoS Comput. Biol., 3, e160.
13. Carrillo, H. and Lipman, D. (1988) The multiple sequence alignment problem in biology. SIAM J. Appl. Math., 48, 1073-1082.
14. Cover, T.M. and Thomas, J.A. (1991) Elements of Information Theory. Wiley, New York, NY.
15. Dayhoff, M.O. et al. (1978)Amodel of evolutionary change in proteins. In Dayhoff, M.O. (ed.) Atlas of Protein Sequence and Structure. Vol. 5, Suppl. 3. Natl. Biomed. Res. Found., Washington, DC, pp. 345-352.
16. Dembo, A. et al. (1994) Limit distribution of maximal non-aligned two-sequence segmental score. Ann. Prob., 22, 2022-2039.
17. Eddy, S.R. et al. (1995) Maximum discrimination hidden Markov models of sequence consensus. J. Comput. Biol., 2, 9-23.
18. Edgar, R.C. (2004a) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res., 32, 1792-1797.
19. Edgar, R.C. (2004b) MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics, 5, 113.
20. Edgar, R.C. (2010) Quality measures for protein alignment benchmarks. Nucleic Acids Res., 38, 2145-2153.
21. Edgar, R.C. and Sjölander, K. (2003) SATCHMO: sequence alignment and tree construction using hidden Markov models. Bioinformatics, 19, 1404-1411.
22. Edgar, R.C. and Sjölander, K. (2004) A comparison of scoring functions for protein sequence profile alignment. Bioinformatics, 20, 1301-1308.
23. Feng, D. and Doolittle, R.F. (1987) Progressive sequence alignment as a prerequisite to correct phylogenetic trees. J. Mol. Evol., 25, 351-360.
24. Gerstein, M. et al. (1994) Volume changes in protein evolution. Appendix: a method to weight protein sequences to correct for unequal representation. J. Mol. Biol., 236, 1067-1078.
25. Gotoh, O. (1995)Aweighting system and algorithm for aligning many phylogenetically related sequences. Comput. Appl. Biosci., 11, 543-551.
26. Gribskov, M. et al. (1987) Profile analysis: detection of distantly related proteins. Proc. Natl Acad. Sci. USA, 84, 4355-4358.
27. Heger, A. and Holm, L. (2001) Picasso: generating a covering set of protein family profiles. Bioinformatics, 17, 272-279.
28. Heger, A. and Holm, L. (2003) Exhaustive enumeration of protein domain families. J. Mol. Biol., 328, 749-767.
29. Henikoff, S. and Henikoff, J.G. (1992) Amino acid substitution matrices from protein blocks. Proc. Natl Acad. Sci. USA, 89, 10915-10919.
30. Henikoff, S. and Henikoff, J.G. (1994) Position-based sequence weights. J. Mol. Biol., 243, 574-578.
31. Karlin, S. and Altschul, S.F. (1990) Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes. Proc. Natl Acad. Sci. USA, 87, 2264-2268.
32. Krogh, A. and Mitchison, G. (1995) Maximum entropy weighting of aligned sequences of protein or DNA. In Rawlings, C. et al. (eds) Proceedings of the Third International Conference Intelligent Systems for Molecular Biology. AAAI Press, Menlo Park, CA, pp. 215-221.
33. Lin, J. (1991) Divergence measures based on the Shannon entropy. IEEE Trans. Informat. Theory, 37, 145-151.
34. Lipman, D.J. et al. (1989) A tool for multiple sequence alignment. Proc. Natl Acad. Sci. USA, 86, 4412-4415.
35. Madera, M. et al. (2004) The SUPERFAMILY database in 2004: additions and improvements. Nucleic Acids Res., 32, D235-D239.
36. Marti-Renom, M.A. et al. (2004) Alignment of protein sequences by their profiles. Protein Sci., 13, 1071-1087.
37. Mittelman, D. et al. (2003) Probabilisitic scoring measures for profile-profile comparison yield more accurate short seed alignments. Bioinformatics, 19, 1531-1539.
38. Murata, M. et al. (1985) Simultaneous comparison of three protein sequences. Proc. Natl Acad. Sci. USA, 82, 3073-3077.
39. Notredame, C. et al. (2000) T-Coffee: a novel method for fast and accurate multiple sequence alignment. J. Mol. Biol., 302, 205-217.
40. Ohlson, T. et al. (2004) Profile-profile methods provide improved fold-recognition: a study of different profile-profile alignment methods. Proteins, 57, 188-197.
41. von Öhsen, N. and Zimmer, R. (2001) Improving profile-profile alignments by log average scoring. In Gascuel, O. and Moret, B.M.E (eds) Proceedings of the First International Workshop on Algorithms in Bioinformatics. Springer, London, UK, pp. 11-26.
42. Panchenko, A.R. (2003) Finding weak similarities between proteins by sequence profile comparison. Nucleic Acids Res., 31, 683-689.
43. Papadopoulos, J.S. and Agarwala R. (2007) COBALT: constraint-based alignment tool for multiple protein sequences. Bioinformatics, 23, 1073-1079.
44. Patthy, L. (1987) Detecting homology of distantly related proteins with consensus sequences. J. Mol. Biol., 198, 567-577.
45. Pietrokovski, S. (1996) Searching databases of conserved sequence regions by aligning protein multiple-alignments. Nucleic Acids Res., 24, 3836-3845.
46. Raghava, G.P. et al. (2003) OXBench: a benchmark for evaluation of protein multiple sequence alignment accuracy. BMC Bioinformatics, 4, 47.
47. Rychlewski, L. et al. (2000) Comparison of sequence profiles. Strategies for structural predictions using sequence information. Protein Sci., 9, 232-241.
48. Sadreyev, R. and Grishin, N. (2003)COMPASS: a tool for comparison of multiple protein alignments with assessment of statistical significance. J. Mol. Biol., 326, 317-336.
49. Sander, C. and Schneider, R. (1991) Database of homology-derived protein structures and the structural meaning of sequence alignment. Proteins, 9, 56-68.
50. Sankoff, D. (1975) Minimal mutation trees of sequences. SIAM J. Appl. Math., 28, 35-42.
51. Sankoff, D. and Cedergren, R.J. (1983) Simultaneous comparison of three or more sequences related by a tree. In Sankoff, D. and Kruskal, J.B. (eds) TimeWarps, String Edits and Macromolecules: The Theory and Practice of Sequence Comparison. Addison-Wesley, Reading, MA, pp. 253-263.
52. Schwartz, R.M. and Dayhoff, M.O. (1978) Matrices for detecting distant relationships. In Dayhoff, M.O. (ed.) Atlas of Protein Sequence and Structure. Vol. 5, Suppl. 3. Natl. Biomed. Res. Found., Washington, DC, pp. 353-358.
53. Sibbald, P.R. and Argos, P. (1990) Weighting aligned protein or nucleic acid sequences to correct for unequal representation. J. Mol. Biol., 216, 813-818.
54. Sjölander, K. et al. (1996) Dirichlet mixtures: a method for improved detection of weak but significant protein sequence homology. Comput. Appl. Biosci., 12, 327-345.
55. Sjölander, K. (1998) Phylogenetic inference in protein superfamilies: analysis of SH2 domains. In Glasgow, J. et al. (eds) Proceedings of the Sixth International Conference Intelligent Systems of Molecular Biology. AAAI Press, Menlo Park, CA, pp. 165-174.
56. Söding, J. (2005) Protein homology detection by HMM-HMM comparison. Bioinformatics, 21, 951-960.
57. Sunyaev, S.R. et al. (1999) PSIC: profile extraction from sequence alignments with position-specific counts of independent observations. Protein Eng., 12, 387-394.
58. Tatusov, R.L. et al. (1994) Detection of conserved segments in proteins: Iterative scanning of sequence databases with alignment blocks. Proc. Natl Acad. Sci. USA, 91, 12091-12095.
59. Taylor, W.R. (1986) Identification of protein sequence homology by consensus template alignment. J. Mol. Biol., 188, 233-258.
60. Taylor, W.R. (1987) Multiple sequence alignment by a pairwise algorithm. Comput. Appl. Biosci., 3, 81-87.
61. Thompson, J.D. et al. (1994a) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22, 4673-4680.
62. Thompson, J.D. et al. (1994b) Improved sensitivity of profile searches through the use of sequence weights and gap excision. Comput. Appl. Biosci., 10, 19-29.
63. Thompson, J.D. et al. (1999) BAliBASE: a benchmark alignment database for the evaluation of multiple alignment programs. Bioinformatics, 15, 87-88.
64. Tomii, K. and Akiyama, Y. (2004) FORTE: a profile-profile comparison tool for protein fold recognition. Bioinformatics, 20, 594-595.
65. Vingron, M. and Sibbald, P.R. (1993) Weighting in sequence space: a comparison of methods in terms of generalized sequences. Proc. Natl Acad. Sci. USA, 90, 8777-8781.
66. van Walle, I. et al. (2004) SABmark - a benchmark for sequence alignment that covers the entire known fold space. Bioinformatics, 21, 1267-1268.
67. Wang, G. and Dunbrack, R.L. (2004) Scoring profile-to-profile sequence alignments. Protein Sci., 13, 1612-1626.
68. Yona, G. and Levitt, M. (2002) Within the twilight zone: a sensitive profile-profile comparison tool based on information theory. J. Mol. Biol., 315, 1257-1275.
69. Zhang, D. and Aravind, L. (2010) Identification of novel families and classification of the C2 domain superfamily elucidate the origin and evolution of membrane targeting activities in eukaryotes. Gene, 469, 18-30.
70. Zhang, D. et al. (2011) A novel immunity system for bacterial nucleic acid degrading toxins and its recruitment in various eukaryotic and DNA viral systems. Nucleic Acids Res., 39, 4532-4552.