IMPALA: Matching a protein sequence against a collection of PSI-BLAST-constructed position-specific score matrices

Bioinformatics

Volumn 15, Issue 12, 1999, Pages 1000-1011

  Schäffer, Alejandro A ^a   Wolf, Yuri I ^a   Ponting, Chris P ^a,c   Koonin, Eugene V ^a   Aravind, L ^b   Altschul, Stephen F ^a  

^a NATIONAL INSTITUTES OF HEALTH   (United States)

^b TEXAS A AND M UNIVERSITY   (United States)

^c UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; PROTEIN;

ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; COMPUTER PROGRAM; DATA BASE; INTERNET; PRIORITY JOURNAL; SEQUENCE HOMOLOGY; STATISTICAL ANALYSIS;

AEPYCEROS MELAMPUS;

EID: 0038438514     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/15.12.1000     Document Type: Article

References (68)

1. Altschul, S.F. and Gish, W. (1996) Local alignment statistics. Methods Enzymol., 266, 460-480.
2. Altschul, S.F. and Koonin, E.V. (1998) Iterated profile searches with PSI-BLAST - a tool for discovery in protein databases. Trends Biochem. Sci., 23, 444-447.
3. Altschul, S.F., Gish, W., Miller, W., Myers, E.W. and Lipman, D.J. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
4. Altschul, S.F., Boguski, M.S., Gish, W. and Wootton, J.C. (1994) Issues in searching molecular databases. Nat. Genet., 6, 119-129.
5. Altschul, S.F., Madden, T.L., Schäffer, A.A., Zhang, J., Zhang, Z., Miller, W. and Lipman, D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
6. Aravind, L. and Koonin, E.V. (1999) Gleaning non-trivial structural, functional and evolutionary information about proteins by iterative database searches. J. Mol. Biol., 287, 1023-1040.
7. Bailey, T.L. and Elkan, C. (1995) The value of prior knowledge in discovering motifs with MEME. In Rawlings, C., Clark, D., Altman, R., Hunter, L., Lengauer, T. and Wodak, S. (eds), Proceedings of the Third International Conference Intelligent Systems for Molecular Biology AAAI Press, Menlo Park, California, pp. 21-29.
8. Bailey, T.L. and Gribskov, M. (1998) Combining evidence using p-values: application to sequence homology searches. Bioinformatics, 14, 48-54.
9. Baldi, P. and Chauvin, Y. (1994) Hidden Markov models of the G-protein-coupled receptor family. J. Comput. Biol., 1, 311-336.
10. Baldi, P., Chauvin, Y., Hunkapiller, T. and McClure, M.A. (1994) Hidden Markov models of biological primary sequence information. Proc. Natl. Acad. Sci. USA, 91, 1059-1063.
11. Bateman, A., Birney, E., Durbin, R., Eddy, S.R., Finn, R.D. and Sonnhammer, E.L.L. (1999) Pfam 3.1: 1313 multiple alignments and profile HMMs match the majority of proteins. Nucleic Acids Res., 27, 260-262.
12. Berg, O.G. and von Hippel, P.H. (1987) Selection of DNA binding sites by regulatory proteins. Statistical-mechanical theory and application to operators and promoters. J. Mol. Biol., 193, 723-750.
13. Brenner, S.E., Chothia, C. and Hubbard, T.J. (1998) Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships. Proc. Natl. Acad. Sci. USA, 95, 6073-6078.
14. Brown, M., Hughey, R., Krogh, A., Mian, I.S., Sjölander, K. and Haussler, D. (1993) Using Dirichlet mixture priors to derive hidden Markov models for protein families. In Hunter, L., Searls, D. and Shavlik, J. (eds), Proceedings of the First International Conference on Intelligent Systems for Molecular Biology AAAI Press, Menlo Park, California, pp. 47-55.
15. Bucher, P., Karplus, K., Moeri, N. and Hofmann, K. (1996) A flexible motif search technique based on generalized profiles. Comput. Chem., 20, 3-23.
16. Chervitz, S.A., Aravind, L., Sherlock, G., Ball, C.A., Koonin, E.V., Dwight, S.S., Harris, M.A., Dolinski, K., Mohr, S., Smith, T., Weng, S., Cherry, J.M. and Botstein, D. (1998) Comparison of the complete protein sets of worm and yeast: orthology and divergence. Science, 282, 2022-2028.
17. Collins, J.F., Coulson, A.F.W. and Lyall, A. (1988) The significance of protein sequence similarities. Comput. Appl. Biosci., 4, 67-71.
18. Dembo, A., Karlin, S. and Zeitouni, O. (1994) Limit distribution of maximal non-aligned two-sequence segmental score. Ann. Prob., 22, 2022-2039.
19. Dodd, I.B. and Egan, J.B. (1987) Systematic method for the detection of potential lambda cro-like DNA-binding regions in proteins. J. Mol. Biol., 194, 557-564.
20. Durbin, R., Eddy,S., Krogh, A. and Mitchison, G. (1998) Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids. Cambridge University Press, Cambridge.
21. Eddy, S.R. (1996) Hidden Markov models. Curr. Opin. Struct. Biol., 6, 361-365.
22. Eddy, S.R. (1998) Profile hidden Markov models. Bioinformatics, 14, 755-763
23. Fischer, D. and Eisenberg, D. (1997) Assigning folds to the proteins encoded by the genome of Mycoplasma genitalium. Proc. Natl. Acad. Sci. USA, 94, 11929-11934.
24. Fraser, C.M., Gocayne, J.D., White, O., Adams, M.D., Clayton, R.A., Fleischmann, R.D., Bult, C.J., Kerlavage, A.R., Sutton, G., Kelley, J.M., Fritchman, J.L., Weidman, J.F., Small, K.V., Sandusky, M., Fuhrmann, J., Nguyen, D, Utterback, T.R., Saudek, D.M., Phillips, C.A., Merrick, J.M., Tomb, J.F., Dougherty, B.A., Bott, K.F., Hu, P.C., Lucier, T.S., Peterson, S.N., Stnith, H.O., Hutchison, C.A. and Venter, J.C. (1995) The minimal gene complement of Mycoplasma genitalium. Science, 270, 397-403.
25. Gish, W. and States, D.J. (1993) Identification of protein coding regions by database similarity search. Nat. Genet., 3, 266-272.
26. Gotoh, O. (1982) An improved algorithm for matching biological sequences. J. Mol. Biol., 162, 705-708.
27. Gribskov, M., McLachlan, A.D. and Eisenberg, D. (1987) Profile analysis: detection of distantly related proteins. Proc. Natl. Acad. Sci. USA, 84, 4355-4358.
28. Gribskov, M., Lüthy, R. and Eisenberg, D. (1990) Profile analysis. Methods Enzymol., 183, 146-159.
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) Protein family classification based on searching a database of blocks. Genomics, 19, 97-107.
31. Henikoff, J.G., Henikoff, S. and Pietrokovski, S. (1999) New features of the blocks database servers. Nucleic Acids Res., 27, 226-228.
32. Hofmann, K., Bücher, P., Falquet, L. and Bairoch, A. (1999) The PROSITE database, its status in 1999. Nucleic Acids Res., 27, 215-219.
33. Hubbard, T.J.P., Ailey, B., Brenner, S.E., Murzin, A.G. and Chothia, C. (1999) SCOP: a structural classification of proteins database. Nucleic Acids Res., 27, 254-256.
34. Huynen, M., Doerks, T., Eisenhaber, F., Orengo, C., Sunyaev, S., Yuan, Y. and Bork, P. (1998) Homology-based fold predictions for Mycoplasma genitalium proteins. J. Mol. Biol., 280, 323-326.
35. 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.
36. Krogh, A., Brown, M., Mian, I.S., Sjölander, K. and Haussler, D. (1994) Hidden Markov models in computational biology. Applications to protein modeling. J. Mol. Biol., 235, 1501-1531.
37. Lawrence, C.E., Altschul, S.F., Boguski, M.S., Liu, J.S., Neuwald, A.F. and Wootton, J.C. (1993) Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment. Science, 262, 208-214.
38. McLachlan, A.D. (1983) Analysis of gene duplication repeats in the myosin rod. J. Mol. Biol., 169, 15-30.
39. Mott, R. (1992) Maximum-likelihood estimation of the statistical distribution of Smith-Waterman local sequence similarity scores. Bull. Math. Biol., 54, 59-75.
40. Murzin, A.G., Brenner, S.E., Hubbard, T. and Chothia, C. (1995) SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol., 247, 536-540.
41. Mushegian, A.R., Bassett, D.E. Jr, Boguski, M.S., Bork, P. and Koonin, E.V. (1997) Positionally cloned human disease genes: patterns of evolutionary conservation and functional motifs. Proc. Natl. Acad. Sci. USA, 94, 5831-5836.
42. Neuwald, A.F., Liu, J.S., Lipman, D.J. and Lawrence, C.E. (1997) Extracting protein alignment models from the sequence database. Nucleic Acids Res., 25, 1665-1677.
43. Park, J., Karplus, K., Barrett, C., Hughey, R., Haussler, D., Hubbard, T. and Chothia, C. (1998) Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods. J. Mol. Biol., 284, 1201-1210.
44. Patthy, L. (1987) Detecting homology of distantly related proteins with consensus sequences. J. Mol. Biol., 198, 567-577.
45. Pearson, W.R. (1998) Empirical statistical estimates for sequence similarity searches. J. Mol. Biol., 276, 71-84.
46. Pearson, W.R. and Lipman, D.J. (1988) Improved tools for biological sequence comparison. Proc. Natl. Acad. Sci. USA, 85, 2444-2448.
47. Ponting, C.P., Aravind, L., Schultz, J., Bork, P. and Koonin, E.V. (1999a) Eukaryotic signalling domain homologues in archaea and bacteria. Ancient ancestry and horizontal gene transfer. J. Mol. Biol., 289, 729-745.
48. Ponting, C.P., Schultz, J., Milpetz, F. and Bork, P. (1999b) SMART: identification and annotation of domains from signalling and extracellular protein sequences. Nucleic Acids Res., 27, 229-232.
49. Rychlewski, L., Zhang, B. and Godzik, A. (1998) Fold and function predictions for Mycoplasma genitalium proteins. Fold. Des., 3, 229-238.
50. Schneider, T.S., Stormo, G.D., Gold, L. and Ehrenfeucht, A. (1986) Information content of binding sites on nucleotide sequences. J. Mol. Biol., 188, 415-431.
51. Smith, T.F. and Waterman, M.S. (1981) Identification of common molecular subsequences. J. Mol. Biol., 147, 195-197.
52. Smith, T.F., Waterman, M.S. and Burks, C. (1985) The statistical distribution of nucleic acid similarities. Nucleic Acids Res., 13, 645-656.
53. 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.
54. Staden, R. (1984) Computer methods to locate signals in nucleic acid sequences. Nucleic Acids Res., 12, 505-519.
55. Sternberg, M.J.E., Bates, P.A., Kelley, L.A. and MacCallum, R.M. (1999) Progress in protein structure prediction: assessment of CASP3. Curr. Opin. Struct. Biol., 9, 368-373.
56. Stormo, G.D. and Hartzell, G.W. III (1989) Identifying protein-binding sites from unaligned DNA fragments. Proc. Natl. Acad. Sci. USA, 86, 1183-1187.
57. Tanaka, H., Ishikawa, M., Asai, K. and Konagawa, A. (1993) Hidden Markov models and iterative aligners: study of their equivalence and possibilities. In Hunter, L., Searls, D. and Shavlik, J. (eds), Proceedings of the First International Conference on Intelligent Systems for Molecular Biology AAAI Press, Menlo Park, CA, pp. 395-401.
58. Tatusov, R.L., Altschul, S.F. and Koonin, E.V. (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. Teichmann, S.A., Park, J. and Chothia, C. (1998) Structural assignments, to the Mycoplasma genitalium proteins show extensive gene duplications and domain rearrangements. Proc. Natl. Acad. Sci. USA, 95, 14658-14663.
61. Teichmann, S.A., Chothia, C. and Gerstein, M. (1999) Advances in structural genomics. Curr. Opin. Struct. Biol., 9, 390-399.
62. Wallace, J.C. and Henikoff, S. (1992) PATMAT: a searching and extraction program for sequence, pattern and block queries and databases. Comput. Appl. Biosci., 8, 249-254.
63. Waterman, M.S. and Eggert, M. (1987) A new algorithm for best subsequence alignments with application to tRNA-rRNA comparisons. J. Mol. Biol., 197, 723-728.
64. Waterman, M.S. and Vingron, M. (1994) Rapid and accurate estimates of statisticalsignificance for sequence database searches. Proc. Natl. Acad. Sci. USA, 91, 4625-4628.
65. Wolf, Y.I., Brenner, S.E., Bash, P.A. and Koonin, E.V. (1999) Distribution of protein folds in the three superkingdoms of life. Genome Res., 9, 17-26.
66. Wootton, J.C. and Federhen, S. (1993) Statistics of local complexity in amino acid sequences and sequence databases. Comput. Chem., 17, 149-163.
67. Yi, T.-M. and Lander, E.S. (1994) Recognition of related proteins by iterative template refinement (ITR). Protein Sci., 3, 1315-1328.
68. Zhang, Z., Berman, P. and Miller, W. (1998) Alignments without low-scoring regions. J. Comput. Biol., 5, 197-210.