Improving accuracy of multiple sequence alignment algorithms based on alignment of neighboring residues

Nucleic Acids Research

Volumn 37, Issue 2, 2009, Pages 463-472

  Lu, Yue ^a   Sze, Sing Hoi ^a  

^a TEXAS A AND M UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; AMINO ACID SEQUENCE; ARTICLE; BASE PAIRING; CONTROLLED STUDY; DNA MODIFICATION; DNA SEQUENCE; GENE STRUCTURE; GENETIC ALGORITHM; INTERMETHOD COMPARISON; PRIORITY JOURNAL; RNA SEQUENCE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS;

ALGORITHMS; REPRODUCIBILITY OF RESULTS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SEQUENCE ANALYSIS, PROTEIN; SEQUENCE ANALYSIS, RNA;

EID: 59649095778     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkn945     Document Type: Article

References (40)

1. Thompson,J.D., Higgins,D.G. and Gibson,T.J. (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, 4673-4680.
2. Notredame,C., Higgins,D.G. and Heringa,J. (2000) T-Coffee: A novel method for fast and accurate multiple sequence alignment. J. Mol. Biol., 302, 205-217.
3. Edgar,R.C. (2004) MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res., 32, 1792-1797.
4. Do,C.B., Mahabhashyam,M.S., Brudno,M. and Batzoglou,S. (2005) ProbCons: probabilistic consistency-based multiple sequence alignment. Genome Res., 15, 330-340.
5. Pei,J. and Grishin,N.V. (2006) MUMMALS: Multiple sequence alignment improved by using hidden Markov models with local structural information. Nucleic Acids Res., 34, 4364-4374.
6. Roshan,U. and Livesay,D.R. (2006) Probalign: Multiple sequence alignment using partition function posterior probabilities. Bioinformatics, 22, 2715-2721.
7. Katoh,K. and Toh,H. (2008) Recent developments in the MAFFT multiple sequence alignment program. Brief. Bioinformatics, 9, 286-298.
8. Gotoh,O. (1996) Significant improvement in accuracy of multiple protein sequence alignments by iterative refinement as assessed by reference to structural alignments. J. Mol. Biol., 264, 823-838.
9. Zhou,H. and Zhou,Y. (2005) SPEM: Improving multiple sequence alignment with sequence profiles and predicted secondary structures. Bioinformatics, 21, 3615-3621.
10. Pei,J. and Grishin,N.V. (2007) PROMALS: Towards accurate multiple sequence alignments of distantly related proteins. Bioinformatics, 23, 802-808.
11. Wilm,A., Higgins,D.G. and Notredame,C. (2008) R-Coffee: A method for multiple alignment of non-coding RNA. Nucleic Acids Res., 36 e52.
12. O'Sullivan,O., Suhre,K., Abergel,C., Higgins,D.G. and Notredame,C. (2004) 3DCoffee: Combining protein sequences and structures within multiple sequence alignments. J. Mol. Biol., 340, 385-395.
13. Van Walle,I., Lasters,I. and Wyns,L. (2004) Align-m - a new algorithm for multiple alignment of highly divergent sequences. Bioinformatics 20, 1428-1435.
14. Pei,J., Kim,B.-H. and Grishin,N.V. (2008) PROMALS3D: A tool for multiple protein sequence and structure alignments. Nucleic Acids Res., 36, 2295-2300.
15. Marti-Renom,M.A., Madhusudhan,M.S. and Sali,A. (2004) Alignment of protein sequences by their profiles. Protein Sci., 13, 1071-1087.
16. Simossis,V.A., Kleinjung,J. and Heringa,J. (2005) Homology-extended sequence alignment. Nucleic Acids Res., 33, 816-824.
17. Spang,R., Rehmsmeier,M. and Stoye,J. (2002) A novel approach to remote homology detection: Jumping alignments. J. Comput. Biol., 9, 747-760.
18. Panchenko,A.R., Kondrashov,F. and Bryant,S. (2004) Prediction of functional sites by analysis of sequence and structure conservation. Protein Sci., 13, 884-892.
19. Capra,J.A. and Singh,M. (2007) Predicting functionally important residues from sequence conservation. Bioinformatics, 23, 1875-1882.
20. Bartlett,G.J., Porter,C.T., Borkakoti,N. and Thornton,J.M. (2002) Analysis of catalytic residues in enzyme active sites. J. Mol. Biol. 324, 105-121.
21. Kabsch,W. and Sander,C. (1983) Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features. Biopolymers, 22, 2577-2637.
22. Gardner,P.P., Wilm,A. and Washietl,S. (2005) A benchmark of multiple sequence alignment programs upon structural RNAs. Nucleic Acids Res. 33, 2433-2439.
23. Huang,X. and Miller,W. (1991) A time-efficient linear-space local similarity algorithm. Adv. Appl. Math., 12, 337-357.
24. Kimura,M. (1983) The Neutral Theory of Molecular Evolution, Cambridge University Press, Cambridge, U.K.
25. Heniko.,S. and Heniko.,J.G. (1992) Amino acid substitution matrices from protein blocks. Proc. Natl Acad. Sci. USA, 89, 10915-10919.
26. Thompson,J.D., Koehl,P., Ripp,R. and Poch,O. (2005) BAliBASE 3.0: Latest developments of the multiple sequence alignment benchmark. Proteins 61, 127-136.
27. Mizuguchi,K., Deane,C.M., Blundell,T.L. and Overington,J.P. (1998) HOMSTRAD: A database of protein structure alignments for homologous families. Protein Sci., 7, 2469-2471.
28. 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.
29. Griffiths-Jones,S., Bateman,A., Marshall,M., Khanna,A. and Eddy,S.R. (2003) Rfam: An RNA family database. Nucleic Acids Res., 31, 439-441.
30. Carroll,H., Beckstead,W., O'Connor,T., Ebbert,M., Clement,M., Snell,Q. and McClellan,D. (2007) DNA reference alignment benchmarks based on tertiary structure of encoded proteins. Bioinformatics, 23, 2648-2649.
31. Thompson,J.D., Plewniak,F. and Poch,O. (1999) A comprehensive comparison of multiple sequence alignment programs. Nucleic Acids Res., 27 2682-2690.
32. Holm,L. and Sander,C. (1998) Dictionary of recurrent domains in protein structures. Proteins, 33, 88-96.
33. Zemla,A., Venclovas,Č., Moult,J. and Fidelis,K. (1999) Processing and analysis of CASP3 protein structure predictions. Proteins, Suppl. 3, 22-29.
34. Venclovas,Č., Zemla,A., Fidelis,K. and Moult,J. (2003) Assessment of progress over the CASP experiments. Proteins, 53, 585-595.
35. Rychlewski,L., Fischer,D. and Elofsson,A. (2003) LiveBench-6: large-scale automated evaluation of protein structure prediction servers. Proteins, 53, 542-547.
36. Wallner,B. and Elofsson,A. (2003) Can correct protein models be identified? Protein Sci., 12, 1073-1086.
37. Zhang,Y. and Skolnick,J. (2004) Scoring function for automated assessment of protein structure template quality. Proteins, 57 702-710.
38. Berman,H.M., Westbrook,J., Feng,Z., Gilliland,G., Bhat,T.N., Weissig,H., Shindyalov,I.N. and Bourne,P.E. (2000) The Protein Data Bank. Nucleic Acids Res., 28, 235-242.
39. Washietl,S., Hofacker,I.L. and Stadler,P.F. (2005) Fast and reliable prediction of noncoding RNAs. Proc. Natl Acad. Sci. USA, 102 2454-2459.
40. Wilcoxon,F. (1947) Probability tables for individual comparisons by ranking methods. Biometrics, 3, 119-122.