Multiple alignment of protein sequences with repeats and rearrangements

Nucleic Acids Research

Volumn 34, Issue 20, 2006, Pages 5932-5942

  Phuong, Tu Minh ^a   Do, Chuong B ^b   Edgar, Robert C ^c   Batzoglou, Serafim ^b  

^a POSTS AND TELECOMMUNICATIONS INSTITUTE OF TECHNOLOGY   (Viet Nam)

^b Stanford University   (United States)

^c NONE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; BIOINFORMATICS; COMPUTER PROGRAM; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DOMAIN; PROTEIN STRUCTURE; SENSITIVITY AND SPECIFICITY; SEQUENCE ALIGNMENT;

ALGORITHMS; COMPUTATIONAL BIOLOGY; INTERNET; PROTEIN STRUCTURE, TERTIARY; REPETITIVE SEQUENCES, AMINO ACID; REPRODUCIBILITY OF RESULTS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN; SOFTWARE;

EID: 33845682909     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkl511     Document Type: Article

References (42)

1. Bateman,A., Coin,L., Durbin,R., Finn,R.D., Hollich,V., Griffiths-Jones,S., Khanna,A., Moxon,M.M., Sonnhammer,E.L., Studholme,D.J. et al. (2004) The Pfam protein families database. Nucleic Acids Res., 32, D138-D141.
2. Phillips,A., Janies,D. and Wheeler,W. (2000) Multiple sequence alignments in phylogenetic analysis. Mol. Phylogenet. Evol., 16, 317-330.
3. Rost,B. and Sander,C. (1994) Combining evolutionary information and neural networks to predict protein secondary structure. Proteins, 19, 55-72.
4. Livingstone,C.D. and Barton,G.J. (1993) Protein sequence alignments: A strategy for the hierarchical analysis of residue conservation. Comput. Appl. Biosci., 9, 745-756.
5. Thompson,J.D., Plewniak,F. and Poch,O. (1999) A comprehensive comparison of multiple sequence alignment programs. Nucleic Acids Res., 27, 2682-2690.
6. Apic,G., Gough,J. and Teichmann,S.A. (2001) Domain combinations in archaeal, eubacterial, and eukaryotiic proteomes. J. Mol. Biol., 310, 311-325.
7. George,R.A. and Heringa,J. (2002) Protein domain identification and improved sequence similarity searching using PSI-BLAST. Proteins, 48, 672-681.
8. Morgenstern,B., Frech,K., Dress,A. and Werner,T. (1998) DIALIGN: Finding local similarities by multiple sequence alignment. Bioinformatics, 14, 290-294.
9. Feng,D.F. and Doolittle,R.F. (1987) Progressive sequence alignment as a prerequisite to correct phylogenetic trees. J. Mol. Evol., 25, 351-360.
10. Do,C.B., Mahabhashyam,M.S.B., Brudno,M. and Batzoglou,S. (2005) ProbCons: Probabilistic consistency-based multiple sequence alignment. Genome Res., 15, 330-340.
11. Pellegrini,M., Marcotte,E.M. and Yeates,T.O. (1999) A fast algorithm for genome-wide analysis of proteins with repeated sequences. Proteins, 35, 440-446.
12. Raphael,B., Zhi,D., Tang,H. and Pevzner,P. (2004) A novel method for multiple alignment of sequences with repeated and shuffled elements. Genome Res., 14, 2336-2346.
13. Smith,T.F. and Waterman,M.S. (1981) Identification of common molecular subsequences. J. Mol. Biol., 147, 195-197.
14. Wheelan,S.J., Marchler-Bauer,A. and Bryant,S.H. (2000) Domain size distributions can predict domain boundaries. Bioinformatics, 16, 613-618.
15. Bahr,A., Thompson,J.D., Thiery,J.-C. and Poch,O. (2001) BAliBASE (Benchmark Alignment dataBASE): Enhancements for repeats, transmembrane sequences and circular permutations. Nucleic Acid Res., 29, 323-326.
16. Durbin,R., Eddy,S.R., Krogh,A. and Mitchison,G. (1998) Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids. Cambridge University Press, Cambridge, UK.
17. Morgenstern,B., Dress,A. and Werner,T. (1996) Multiple DNA and protein sequence alignment based on segment-to-segment comparison. Proc. Natl Acad. Sci. USA, 93, 12098-12103.
18. Brocchieri,L. and Karlin,S. (1998) A symmetric-iterated method for the multiple alignment of protein sequences. J. Mol. Biol., 276, 249-264.
19. Edgar,R.C. and Sjölander,K. (2003) SATCHMO: Sequence alignment and tree construction using hidden Markov models. Bioinformatics, 19, 1404-1411.
20. Lee,C., Grasso,C. and Sharlow,M.F. (2002) Multiple sequence alignment using partial order graphs. Bioinformatics, 18, 452-464.
21. Bailey,T.L. and Elkan,C. (1994) Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc. Int. Conf. Intell. Syst. Mol. Biol., 2, 28-36.
22. Hertz,G.Z. and Stormo,G.D. (1999) Identifying DNA and protein patterns with statistically significant alignments of multiple sequences. Bioinformatics, 15, 563-577.
23. 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.
24. 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.
25. Altschul,S.F., Madden,T.L., Schaffer,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.
26. Schuler,G.D., Altschul,S.F. and Lipman,D.J. (1991) A workbench for multiple alignment construction and analysis. Proteins, 9, 180-190.
27. Sonnhammer,E.L.L. and Kahn,D. (1994) Modular arrangement of proteins as inferred from analysis of homology. Protein Sci., 3, 482-492.
28. Bru,C., Courcelle,E., Carrère,S., Beausse,Y., Dalmar,S. and Kahn,D. (2005) The ProDOm database of protein domain families: More emphasis on 3D. Nucleic Acids Res., 33, D212-D215.
29. Notredame,C. (2001) Mocca: Semi-automatic method for domain hunting. Bioinformatics, 17, 373-374.
30. Heger,A. and Holm,L. (2000) Rapid automatic detection and alignment of repeats in protein sequences. Proteins, 41, 224-237.
31. Heringa,J. and Argos,P. (1993) A method to recognize distant repeats in protein sequences. Proteins, 17, 391-401.
32. Szklarczyk,R. and Heringa,J. (2004) Tracking repeats using significance and transitivity. Bioinformatics, 20, I311-I317.
33. Sammeth,M. and Heringa,J. (2006) Global multiple-sequence alignment with repeats. Proteins, 64, 263-274.
34. Waterman,M.S. and Eggert,M. (1987) A new algorithm for best subsequence alignments with application to tRNA-tRNA comparisons. J. Mol. Biol., 197, 723-728.
35. Morgenstern,B. (1999) DIALIGN 2: Improvement of the segment-to-segment approach to multiple sequence alignment. Bioninformatics, 15, 211-218.
36. Subramanian,A.R., Weyer-Menkhoff,J., Kaufmann,M. and Morgenstern,B. (2005) DIALIGN-T: An improved algorithm for segment-based multiple sequence alignment. BMC Bioinformatics, 6, 66.
37. 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.
38. Edgar,R.C. (2004) MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res., 32, 1792-1797.
39. Henikoff,S. and Henikoff,J.G. (1992) Amino acid substitution matrices from protein blocks. Proc. Natl Acad. Sci. USA, 89, 10915-10919.
40. Thompson,J.D., Plewniak,F. and Poch,O. (1999) BAliBASE: A benchmark alignment database for the evaluation of multiple alignment programs. Bioinformatics, 15, 87-88.
41. Nagarajan,N. and Yona,G. (2004) Automatic prediction of protein domains from sequence information using a hybrid learning system. Bioinformatics, 20, 1335-1360.
42. Sonnhammer,E.L.L., Eddy,S.R., Birney,E., Bateman,A. and Durbin,R. (1998) Pfam: Multiple sequence alignments and HMM-profiles of protein domains. Nucleic Acids Res., 26, 320-322.