SPEM: Improving multiple sequence alignment with sequence profiles and predicted secondary structures

Bioinformatics

Volumn 21, Issue 18, 2005, Pages 3615-3621

  Zhou, Hongyi ^a   Zhou, Yaoqi ^a,b  

^a UNIVERSITY AT BUFFALO   (United States)

^b FUDAN UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ALGORITHM; ARTICLE; BIOINFORMATICS; COMPUTER PROGRAM; CONTROLLED STUDY; EVOLUTION; GENETIC ANALYSIS; INTERMETHOD COMPARISON; MATHEMATICAL COMPUTING; PREDICTION; PRIORITY JOURNAL; PROTEIN SECONDARY STRUCTURE; SCORING SYSTEM; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY;

EID: 24644512819     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/bti582     Document Type: Article

References (60)

1. 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.
2. Attwood,T.K. (2002) The PRINTS database: A resource for identification of protein families. Brief Bioinformatics, 3, 252-263.
3. Boutonnet,N.S. et al. (1995) Optimal protein structure alignments by multiple linkage clustering: Application to distantly related proteins. Protein Eng., 8, 647-662.
4. Brocchieri,L. and Karlin,S. (1998) Asymmetric-iterated multiple alignment of protein sequences. J. Mol. Biol., 276, 249-264.
5. Bucka-Lassen,K. et al. (1999) Combining many multiple alignments in one improved alignment. Bioinformatics, 15, 122-130.
6. Dayhoff,M.O., Schwartz,R.M. and Orcutt,B.C. (1978) A model of evolutionary change in proteins. In Atlas of Proteins Sequences and Structure. National Biomedical Research Foundation, Washington, DC, Vol. 5, pp. 345-352.
7. Devereux,J. et al. (1984) GCG package. Nucleic Acids Res., 22, 387-395.
8. Do,C.B. et al. (2005) Probabilistic consistency-based multiple sequence alignment. Genome Res., 15, 330-340.
9. Domingues,F.S. et al. (2000) Structure-based evaluation of sequence comparison and fold recognition alignment accuracy. J. Mol. Biol., 297, 1003-1013.
10. Eddy,S.R. (1995) Multiple alignment using hidden Markov models. In Third International Conference on Intelligent Systems for Molecular Biology (ISMB). AAAI Press, Cambridge, England, Menlo Park, CA.
11. Edgar,R.C. (1994) MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res., 32, 1792-1797.
12. Edgar,R.C. and Sjölander,K. (2003) SATCHMO: Sequence alignment and tree construction using hidden Markov models. Bioinformatics, 19, 1404-1411.
13. Fischer,D. and Eisenberg,D. (1996) Protein fold recognition using sequence-derived predictions. Protein Sci., 5, 947-955.
14. Goebel,U. et al. (1994) Correlated mutations and residue contacts in proteins. Proteins, 18, 309-317.
15. Gotoh,O. (1982) Significant improvement in accuracy of multiple protein sequence alignments by iterative refinements as assessed by reference to structural alignments. J. Mol. Biol., 264, 823-838.
16. Gribskov,M. et al. (1987) Profile analysis: Detection of distantly related proteins. Proc. Natl Acad. Sci. USA, 84, 4355-4358.
17. Heringa,J. (1999) Two strategies for sequence comparison: profile-preprocessed and secondary-structure-induced multiple alignment. Comput. Chem., 23, 341-364.
18. Hogeweg,P. and Hesper,B. (1984) The alignment of sets of sequences and the construction of phylogenetic trees. An integrated method. J. Mol. Evol., 20, 175-186.
19. Holm,L. and Sander,C. (1994) The FSSP database of structurally aligned protein fold families. Nucleic Acids Res., 22, 3600-3609.
20. Hughey,R. and Krogh,A. (1996) Hidden Markov models for sequence analysis: Extension and analysis of the basic method. Comput. Appl. Biol. Sci., 12, 95-107.
21. Jones,D.T. (1999) Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol., 292, 195-202.
22. Kabsch,W. (1978) A discussion of the solution for the best rotation to relate two sets of vectors. Acta Cyrstallogr. A, 34, 827-828.
23. Kabsch,W. and Sander,C. (1983) Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features. Biopolymers, 22, 2577-2637.
24. Katoh,K. et al. (2005) MAFFT version 5: Improvement in accuracy of multiple sequence alignment. Nucleic Acids Res., 33, 511-518.
25. Kolodny,R. et al. (2005) Comprehensive evaluation of protein structure alignment methods: Scoring by geometric measures. J. Mol. Biol., 346, 1173-1188.
26. Koretke,K.K. et al. (2001) Fold recognition from sequence comparisons. Proteins, Suppl. 5, 68-75.
27. Lipman,D.J. et al. (1989) A tool for multiple sequence alignment. Proc. Natl Acad. Sci. USA, 86, 4412-4415.
28. Mizuguchi,K. et al. (1998) HOMSTRAD: A database of protein structure alignments for homologous families. Protein Sci., 7 2469-2471.
29. Morgenstern,B. et al. (1996) Multiple DNA and protein sequence based on segment-to-segment comparison. Proc. Natl Acad. Sci. USA, 93, 12098-12103.
30. Needleman,S.B. and Wunsch,C.D. (1970) A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol., 48, 443-453.
31. Notredame,C. (2002) Recent progress in multiple sequence alignment: A survey. Pharmacogenomics, 3, 131-144.
32. Notredame,C. and Higgins,D.G. (1996) SAGA: Sequence alignment by genetic algorithm. Nucleic Acids Res., 4, 1515-1524.
33. Notredame,C. et al. (1998) COFFEE: An objective function for multiple sequence alignments. Bioinformatics, 14, 407-422.
34. O'Sullivan,O. et al. (2004) 3DCoffee: Combining protein sequences and structures within multiple sequence alignments. J. Mol. Biol., 340, 385-395.
35. Pei,J. et al. (2003) PCMA: Fast and accurate multiple sequence alignment based on profile consistency. Bioinformatics, 19, 427-428.
36. Press,W.H. et al. (1992) Numerical Recipes. The Art of Scientific Computing, 2nd edn. Cambridge University Press, Cambridge, UK.
37. Rost,B. et al. (1994) PHD-an automatic server for protein secondary structure prediction. Comput. Appl. Biosci., 10, 53-60.
38. Russell,R.B. and Barton,G.J. (1992) Multiple protein sequence alignment from tertiary structure comparison. Proteins, 14, 309-323.
39. Rychlewski,L. et al. (2000) Comparison of sequence profiles. strategies for structural predictions using sequence information. Protein Sci., 9, 232-241.
40. Saitou,N. and Nei,M. (1987) The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol., 4, 406-425.
41. Sali,A. and Blundell,T.L. (1990) Definition of general topological equivalence in protein structures. a procedure involving comparison of properties and relationships through simulated annealing and dynamic programming. J. Mol. Biol., 212, 403-428.
42. Shi,J. et al. (2001) FUGUE: Sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties. J. Mol. Biol., 310, 243-257.
43. Shindyalov,I.N. and Bourne,P. (1998) Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Eng, 11, 739-747.
44. Simossis,VA. et al. (2005) Homolog-extended sequence alignment. Nucleic Acids Res., 33, 816-824.
45. Skolnick,J. and Kihara,D. (2001) Defrosting the frozen approximation: PROSPECTOR - a new approach to threading. Proteins, 42, 319-331.
46. Stoye,J. et al. (1997) DCA: An efficient implementation of the divide-and-conquer approach to simultaneous multiple sequence alignment. Comput. Appl. Biosci., 13, 625-626.
47. Sutcliffe,M.J. et al. (1987) Protein Eng., 1, 377-384.
48. Taylor,W.R. and Brown,N.P. (1999) Iterated sequence databank search methods. Comput. Chem., 23, 365-385.
49. Taylor,W.R. and Orengo,C.A. (1989) Protein structure alignment. J. Mol. Biol., 128, 1-22.
50. Thompson,J. et al. (1994) 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, 4673-4690.
51. Thompson,J.D. et al. (1999) A comprehensive comparison of multiple sequence alignment programs. Nucleic Acids Res., 27, 2682-2690.
52. Wallace,I.M. et al. (2005) Evaluation of iterative alignment algorithms for multiple alignment. Bioinformatics, 21, 1408-1414.
53. Walle,I.V. et al. (2005) SABmark - a benchmark for sequence alignment that covers the entire known fold space. Bioinformatics, 21, 1267-1268.
54. Wang,G. and Dunbrack,R.L., Jr. (2004) Scoring profile-to-profile sequence alignments. Protein Sci., 13, 1612-1626.
55. Wang,Y. and Li,K.B. (2004) An adaptive and iterative algorithm for refining multiple sequence alignment. Comput. Biol. Chem., 28 141-148.
56. Xu,Y. and Xu,D. (2000) Protein threading using PROSPECT: Design and evaluation. Proteins, 40, 343-354.
57. 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.
58. Zhou,H. and Zhou,Y. (2004) Single-body knowledge-based energy score combined with sequence-profile and secondary structure information for fold recognition. Proteins, 55, 1005-1013.
59. Zhou,H. and Zhou,Y. (2005a) Fold recognition by combining sequence profiles derived from evolution and from depth-dependent structural alignment of fragments. Proteins, 58, 321-328.
60. 3 servers in CASP 6. Proteins (CASP Suppl. Issue), (in press).