Finding the balance between the mathematical and biological optima in multiple sequence alignment

Trends in Evolutionary Biology

Volumn 2, Issue 1, 2010, Pages 39-48

  Anisimova, Maria ^a,b   Cannarozzi, Gina M ^a,b   Liberles, David A ^c  

^a ETH ZURICH   (Switzerland)

^b SWISS INSTITUTE OF BIOINFORMATICS   (Switzerland)

^c UNIVERSITY OF WYOMING   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 80052262050     PISSN: 20362641     EISSN: 2036265X     Source Type: Journal    
DOI: 10.4081/eb.2010.e7     Document Type: Review

References (125)

1. Morrison DA. Why would phylogeneticists ignore computerized sequence alignment? Syst Biol 2009;58:150-158.
2. Zuckerkandl E, Pauling L. Molecules as documents of evolutionary history. J Theor Biol 1965;8:357-66.
3. Liberles DA, Dittmar K. Characterizing gene family evolution. Biol Proced Online 2008;10:66-73.
4. Illergård K, Ardell DH, Elofsson A. Structure is three to ten times more conserved than sequence - a study of structural response in protein cores. Proteins 2009;77:499-508.
5. Chothia C, Lesk AM. The evolution of protein structures. Cold Spring Harb Symp Quant Biol 1987;52399-405.
6. Durbin R, Eddy S, Krogh A, Mitchison G. Biological sequence analysis: probabilistic models of proteins and nucleic acids. Cambridge University Press;1998.
7. Thompson JD, Higgins DG, Gibson TJ. Improved sensitivity of profile searches through the use of sequence weights and gap excision. Comput Appl Biosci 1994;10:19-29.
8. Lee C, Grasso C, Sharlow MF. Multiple sequence alignment using partial order graphs. Bioinformatics 2002;18:452-64.
9. Löytynoja A, Goldman N. A model of evolution and structure for multiple sequence alignment. Philos Trans R Soc Lond B Biol Sci 2008;363:3913-9.
10. Löytynoja A, Goldman N. Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis. Science 2008;320:1632-5.
11. Kim K, Kim M, Woo Y. A DNA sequence alignment algorithm using quality information and a fuzzy inference method. Prog Nat Sci 2008;18:595-602.
12. Schneider A, Cannarozzi GM, Gonnet GH. Empirical codon substitution matrix. BMC Bioinformatics 2005;6:134.
13. Doron-Faigenboim A, Pupko T. A combined empirical and mechanistic codon model. Mol Biol Evol 2007;24:388-97.
14. Anisimova M, Kosiol C. Investigating protein- coding sequence evolution with probabilistic codon substitution models. Mol Biol Evol 2009;26:255-71.
15. Kosiol C, Holmes I, Goldman N. An empirical codon model for protein sequence evolution. Mol Biol Evol 2007;24:1464-79.
16. Katoh K, Asimenos G, Toh H. Multiple alignment of DNA sequences with MAFFT. Methods Mol Biol (Clifton, N.J.) 2009;537: 39-64.
17. Hofacker IL, Bernhart SHF, Stadler PF. Alignment of RNA base pairing probability matrices. Bioinformatics 2004;20:2222-7.
18. Notredame C, O'Brien EA, Higgins DG. RAGA: RNA sequence alignment by genetic algorithm. Nucleic Acids Res 1997;25: 4570-80.
19. Blanco E, Guigó R, Messeguer X. Multiple non-collinear TF-map alignments of promoter regions. BMC Bioinformatics 2007;8:138.
20. Phuong TM, Do CB, Edgar RC, Batzoglou S. Multiple alignment of protein sequences with repeats and rearrangements. Nucleic Acids Res 2006;34:5932-42.
21. Poirot O, Suhre K, Abergel C, et al.3DCoffee@igs: a web server for combining sequences and structures into a multiple sequence alignment. Nucleic Acids Res 2004;32:W37-40.
22. Pei J, Grishin NV. MUMMALS: multiple sequence alignment improved by using hidden Markov models with local structural information. Nucleic Acids Res 2006;34:4364-74.
23. Subramanian AR, Hiran S, Steinkamp R, et al. DIALIGN-TX and multiple protein alignment using secondary structure information at GOBICS. Nucleic Acids Res 2010;38:1-4.
24. Kececioglu J, Kim E, Wheeler T. Aligning protein sequences with predicted secondary structure. J Comput Biol 2010;17:561-80.
25. Bremges A, Schirmer S, Giegerich R. Fine-tuning structural RNA alignments in the twilight zone. BMC Bioinformatics 2010;11:222.
26. Do CB, Mahabhashyam MSP, Brudno M, Batzoglou S. ProbCons: Probabilistic consistency- based multiple sequence alignment. Genom Res 2005;15:330-40.
27. Bradley RK, Roberts A, Smoot M, et al. Fast statistical alignment. PLoS Comput Biol 2009;5:e1000392.
28. Ahola V, Aittokallio T, Vihinen M, Uusipaikka E. A statistical score for assessing the quality of multiple sequence alignments. BMC Bioinfor - matics 2006;7:484.
29. Penn O, Privman E, Landan G, et al. An alignment confidence score capturing robustness to guide-tree uncertainty. Mol Biol Evol 2010;27:1759-1767.
30. Katoh K, Misawa K, Kuma Ki, Miyata T. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res 2002;30: 3059-66.
31. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004;32: 1792-7.
32. Pandit SB, Skolnick J. Fr-TM-align: a new protein structural alignment method based on fragment alignments and the TM-score. BMC Bioinformatics 2008;9: 531.
33. Gille C, Frömmel C. STRAP: editor for STRuctural Alignments of Proteins. Bioinformatics. 2001;17:377-8.
34. Bahr A, Thompson JD, Thierry JC, Poch O. BAliBASE (Benchmark Alignment dataBASE): enhancements for repeats, transmembrane sequences and circular permutations. Nucleic Acids Res 2001;29:323-6.
35. Mizuguchi K, Deane CM, Blundell TL, Overington JP. HOMSTRAD: a database of protein structure alignments for homologous families. Protein science. 1998;7: 2469-71.
36. Raghava GPS, Searle SMJ, Audley PC, et al. OXBench: a benchmark for evaluation of protein multiple sequence alignment accuracy. BMC Bioinformatics 2003;4:47.
37. Subramanian A, Weyer-Menkhoff J, Kaufmann M, Morgenstern B. DIALIGN-T: an improved algorithm for segment-based multiple sequence alignment. BMC Bioinformatics. 2005;6: 66.
38. Lassmann T, Sonnhammer EL. Automatic extraction of reliable regions from multiple sequence alignments. BMC Bio - informatics 2007;8:S9.
39. Dessimoz C, Gil M. Phylogenetic assessment of alignments reveals neglected tree signal in gaps. Genome Biol 2010;11:R37.
40. J. Multiple sequence alignment with the divide-and-conquer method. Gene 1998; 211GC45-56.
41. Lee C, Grasso C, Sharlow MF. Multiple sequence alignment using partial order graphs. Bioinformatics 2002;18:452-64.
42. Kemena C, Notredame C. Upcoming challenges for multiple sequence alignment methods in the high-throughput era. Bioinformatics 2009; 25:2455-65.
43. Huzurbazar S, Kolesov G, Massey SE, et al. Lineage-specific differences in the amino acid substitution process. J Mol Biol 2010;396:1410-21.
44. Rokas A, Carroll SB. Frequent and widespread parallel evolution of protein sequences. Mol Biol Evol 2008;25:1943-53.
45. Whelan S, Liò P, Goldman N. Molecular phylogenetics: state-of-the-art methods for looking into the past. Trends Genet 2001;17:262-72.
46. Löytynoja A, Goldman N. An algorithm for progressive multiple alignment of sequences with insertions. Proc Natl Acad Sci U S A 2005;102:10557-62.
47. Wang L, Jiang T. On the complexity of multiple sequence alignment. J Comput Biol 1994;1:337-48.
48. Wallace I, O'Sullivan O, Higgins D. MCoffee: combining multiple sequence alignment methods with T-Coffee. Nucleic Acids Res 2006;4:1692-9.
49. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 2000;17:540-52.
50. Talavera G, Castresana J. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst Biol 2007;56: 564.
51. Massey SE, Churbanov A, Rastogi S, Liberles DA. Characterizing positive and negative selection and their phylogenetic effects. Gene 2008;418:22-6.
52. Chang MSS, Benner SA. Empirical analysis of protein insertions and deletions determining parameters for the correct placement of gaps in protein sequence alignments. J Mol Biol 2004;341:617-31.
53. Ponting CP, Lunter G. Signatures of adaptive evolution within human non-coding sequence. Human Molecular Genetics 2006;15:R170-5.
54. Lunter G, Ponting C, Hein J. Genomewide identification of human functional DNA using a neutral indel model. PLoS Comput Biol 2006;2:e5.
55. Creer S. Choosing and using introns in molecular phylogenetics. Evol Bioinform 2007;3:99-108.
56. Thorne J, Kishino H, Felsenstein J. An evolutionary model for maximum likelihood alignment of DNA sequences. J Mol Evol 1991;33:114-24.
57. Thorne JL, Kishino H, Felsenstein J. Inching toward reality: an improved likelihood model of sequence evolution. J Mol Evol 1992;34:3-16.
58. Thorne J, Choi S, Yu J, et al. Population genetics without intraspecific data. Mol Biol Evol 2007;24:1667-77.
59. Higgs PG. Compensatory neutral mutations and the evolution of RNA. Genetica 1998;102-103:91-101.
60. Yang Z, Nielsen R. Mutation-selection models of codon substitution and their use to estimate selective strengths on codon usage. Mol Biol Evol 2008;25:568-79.
61. Taverna DM, Goldstein RA. Why are proteins marginally stable? Proteins 2002;46:105-9.
62. DePristo MA, Weinreich DM, Hartl DL. Missense meanderings in sequence space: a biophysical view of protein evolution. Nat Rev Genet 2005;6:678-87.
63. Rastogi S, Reuter N, Liberles DA. Evaluation of models for the evolution of protein sequences and functions under structural constraint. Biophys Chem 2006;124:134-44.
64. Robinson DM, Jones DT, Kishino H, et al. Protein evolution with dependence among codons due to tertiary structure. Mol Biol Evol 2003;20:1692-704.
65. Henikoff S, Henikoff JG. Performance evaluation of amino acid substitution matrices. Proteins 1993;17:49-61.
66. Dayhoff MO, Schwartz RM, Orcutt BC. A model of evolutionary change in proteins. Atlas of Protein Sequence and Structure 1978;5:345-352.
67. Savill NJ, Hoyle DC, Higgs PG. RNA sequence evolution with secondary structure constraints: comparison of substitution rate models using maximum-likelihood methods. Genetics 2001;157:399-411.
68. Le SQ, Gascuel O. An improved general amino acid replacement matrix. Mol Biol Evol 2008;25:1307-20.
69. Abascal F, Posada D, Zardoya R. MtArt: a new model of amino acid replacement for Arthropoda. Mol Biol Evol 2007;24:1-5.
70. Adachi J, Hasegawa M. Model of amino acid substitution in proteins encoded by mitochondrial DNA. J Mol Evol 1996;42: 459-68.
71. Yang Z, Nielsen R, Hasegawa M. Models of amino acid substitution and applications to mitochondrial protein evolution. Mol Biol Evol 1998;15:1600-11.
72. Dimmic M, Rest J, Mindell D. rtREV: an amino acid substitution matrix for inference of retrovirus and reverse transcriptase phylogeny. J Mol Evol 2002;55:65-73.
73. Muller T, Rahmann S, Rehmsmeier M. Non-symmetric score matrices and the detection of homologous transmembrane proteins. Bioinformatics 2001;17:S182-S189.
74. Rice D, Eisenberg D. A 3D-1D substitution matrix for protein fold recognition that includes predicted secondary structure of the sequence1. J Mol Evol 1997; 267:1026-38.
75. Gong S, Blundell TL. Discarding functional residues from the substitution table improves predictions of active sites within three-dimensional structures. PLoS Comput Biol 2008;4:e1000179.
76. Goonesekere NCW, Lee B. Context-specific amino acid substitution matrices and their use in the detection of protein homologs. Proteins 2008;71:910-9.
77. Koshi JM, Goldstein RA. Context-dependent optimal substitution matrices. Protein Eng 1995;8:641-5.
78. Huang YM, Bystroff C. Improved pairwise alignments of proteins in the Twilight Zone using local structure predictions. Bioinformatics 2006;22:413-22.
79. Biegert A, Söding J. Sequence contextspecific profiles for homology searching. Proc Natl Acad Sci U S A 2009;106:3770-5.
80. Soyer OS, Dimmic MW, Neubig RR, Goldstein RA. Dimerization in aminergic G-protein-coupled receptors: application of a hidden-site class model of evolution. Biochemistry 2003;42:14522-31.
81. Rivas E, Eddy SR. Probabilistic phylogenetic inference with insertions and deletions. PLoS Comput Biol 2008;4:e1000172.
82. Miklós I, Lunter GA, Holmes I. A Long Indel model for evolutionary sequence alignment. Mol Biol Evol 2004;21:529-40.
83. Gotoh O. An improved algorithm for matching biological sequences. J Mol Evol 1982;162;705-8.
84. Edgar RC, Batzoglou S. Multiple sequence alignment. Curr Opin Struct Biol 2006;16:368-73.
85. Benner SA, Cohen MA, Gonnet GH. Empirical and structural models for insertions and deletions in the divergent evolution of proteins. J Mol Evol 1993;229:1065-82.
86. Qian B, Goldstein RA. Distribution of Indel lengths. Proteins 2001;45:102-4.
87. Bradley RK, Holmes I. Transducers: an emerging probabilistic framework for modeling indels on trees. Bioinformatics 2007;23:3258-62.
88. Holmes I. Using guide trees to construct multiple-sequence evolutionary HMMs. Bioinformatics 2003;19:i147-57.
89. Rivas E. Evolutionary models for insertions and deletions in a probabilistic modeling framework. BMC Bioinformatics 2005;6:63.
90. Wong KM, Suchard MA, Huelsenbeck JP. Alignment uncertainty and genomic analysis. Science 2008;319:473-6.
91. Liu K, Raghavan S, Nelesen S, et al. Rapid and accurate large-scale coestimation of sequence alignments and phylogenetic trees. Science 2009;324:1561-4.
92. Redelings BD, Suchard MA. Joint Bayesian estimation of alignment and phylogeny. Syst Biol 2005;54:401-18.
93. Yue F, Shi J, Tang J. Simultaneous phylogeny reconstruction and multiple sequence alignment. BMC Bioinformatics 2009;10:S11.
94. Edgar RC, Sjölander K. SATCHMO: sequence alignment and tree construction using hidden Markov models. Bioinformatics 2003;19:1404-11.
95. Varon A, Vinh LS, Wheeler WC. POY version 4: phylogenetic analysis using dynamic homologies. Cladistics 2010;26: 72-85.
96. Suchard MA, Redelings BD. BAli-Phy: simultaneous Bayesian inference of alignment and phylogeny. Bioinformatics 2006;22:2047-8.
97. Novák A, Miklós I, Lyngsø R, Hein J. StatAlign: an extendable software package for joint Bayesian estimation of alignments and evolutionary trees. Bioinformatics. 2008;24:2403-4.
98. Satija R, Novák A, Miklós I, et al. BigFoot: Bayesian alignment and phylogenetic footprinting with MCMC. BMC Evol Biol 2009;9:217.
99. Fleissner R, Metzler D, von Haeseler A. Simultaneous statistical multiple alignment and phylogeny reconstruction. Systematic Biology 2005;54:548-61.
100. Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 2006;22:2688-90.
101. Giribet G, Wheeler WC, Muona J. DNA multiple sequence alignments. EXS 2002;107-14.
102. Aurahs R, Göker M, Grimm GW, et al. Using the Multiple Analysis Approach to Reconstruct Phylogenetic Relationships among Planktonic Foraminifera from Highly Divergent and Length-polymorphic SSU rDNA Sequences. Bioinformatics and Biology Insights. 2009;3:155-77.
103. Aris-Brosou S. How Bayes tests of molecular phylogenies compare with frequentist approaches. Bioinformatics 2003;19: 618-24.
104. Trapnell C, Salzberg SL. How to map billions of short reads onto genomes. Nature Biotechnology. 2009;27:455-7.
105. Chaisson MJ, Brinza D, Pevzner P. De novo fragment assembly with short matepaired reads: Does the read length matter? Genome Res 2009;19:336-46.
106. Brudno M, Malde S, Poliakov A, et al. Glocal alignment: finding rearrangements during alignment. Bioinformatics 2003;19:i54-62.
107. Paten B, Herrero J, Beal K, et al. Enredo and Pecan: genome-wide mammalian consistency-based multiple alignment with paralogs. Genome research. 2008; 18:1814-28.
108. Paten B, Herrero J, Beal K, Birney E. Sequence progressive alignment, a framework for practical large-scale probabilistic consistency alignment. Bioinfor - matics 2009;25:295-301.
109. Brudno M, Do CB, Cooper GM, et al. LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA. Genome Res 2003;13:721-31.
110. Paten B, Herrero J, Fitzgerald S, et al. Genome-wide nucleotide-level mammalian ancestor reconstruction. Genome Res 2008;18:1829-43.
111. Larkin M, Blackshields G, Brown N, Chenna P. Clustal W and Clustal X version 2.0. Bioinformatics 2007;23:2947-8.
112. Notredame C, Holm L, Higgins D. COFFEE: an objective function for multiple sequence alignments. Bioinformatics 1998;14:407-22.
113. Notredame C, Higgins D, Heringa J. T-coffee: a novel method for fast and accurate multiple sequence alignment1. J Mol Biol 2000;8:205-17.
114. Grasso C, Lee C. Combining partial order alignment and progressive multiple sequence alignment increases alignment speed and scalability to very large alignment problems. Bioinformatics 2004;20: 1546-56.
115. Nuin PAS, Wang Z, Tillier ERM. The accuracy of several multiple sequence alignment programs for proteins. BMC Bioinformatics 2006;7:471.
116. Roshan U, Livesay DR. Probalign: multiple sequence alignment using partition function posterior probabilities. Bioinformatics 2006;22:2715-21.
117. Pei J, Grishin NV. PROMALS: towards accurate multiple sequence alignments of distantly related proteins. Bioinformatics 2007;23:802-8.
118. Wilm A, Higgins DG, Notredame C. RCoffee: a method for multiple alignment of non-coding RNA. Nucl. Acids Res 2008; 36:e52.
119. O'Sullivan O, Suhre K, Abergel C, et al. 3DCoffee: combining protein sequences and structures within multiple sequence alignments. J Mol Biol 2004;340:385-95.
120. Armougom F, Moretti S, Poirot O, et al. Expresso: automatic incorporation of structural information in multiple sequence alignments using 3D-Coffee. Nucl Acids Res 2006;34:W604-8.
121. Heringa J. Local weighting schemes for protein multiple sequence alignment. Comput Chem 2002;26:459-477.
122. Heringa J. Two strategies for sequence comparison: profile-preprocessed and secondary structure-induced multiple alignment. Comput Chem 1999;23:341-64.
123. Pirovano W, Feenstra KA, Heringa J. PRALINETM: a strategy for improved multiple alignment of transmembrane proteins. Bioinformatics 2008;24:492-7.
124. Sahraeian SME, Yoon BJ. PicXAA: greedy probabilistic construction of maximum expected accuracy alignment of multiple sequences. Nucl Acids Res 2010;38:4917-28.
125. Margulies EH, Cooper GM, Asimenos G, et al. Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. Genome Res 2007;17:760-74.