Multiple sequence alignment accuracy and evolutionary distance estimation

BMC Bioinformatics

Volumn 6, Issue , 2005, Pages

  Rosenberg, Michael S ^a  

^a ARIZONA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALIGNMENT ACCURACY; COMPARATIVE GENOMICS; DISTANCE ESTIMATION; EVOLUTIONARY DISTANCE; MULTIPLE ALIGNMENT; MULTIPLE SEQUENCE ALIGNMENTS; SEQUENCE ALIGNMENTS; SIMULATION ANALYSIS;

BIOINFORMATICS; FORESTRY;

ESTIMATION;

ARTICLE; BIOINFORMATICS; COMPUTER PROGRAM; CONTROLLED STUDY; DNA SEQUENCE; GENE DELETION; GENE INSERTION; GENE SEQUENCE; GENETIC ALGORITHM; GENETIC CONSERVATION; NONHUMAN; PHYLOGENETIC TREE; PHYLOGENY; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY; STATISTICAL ANALYSIS; STATISTICAL SIGNIFICANCE; TAXONOMY; ALGORITHM; ANIMAL; BIOLOGY; COMPUTER ANALYSIS; COMPUTER SIMULATION; EVALUATION STUDY; GENE EXPRESSION PROFILING; GENOME; HUMAN; MOLECULAR EVOLUTION; NUCLEOTIDE SEQUENCE; PROCEDURES; PROTEIN DATABASE; PROTEIN MOTIF; REPRODUCIBILITY; SEQUENCE ANALYSIS;

PROTEIN;

ALGORITHMS; AMINO ACID MOTIFS; ANIMALS; BASE SEQUENCE; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; COMPUTING METHODOLOGIES; DATABASES, PROTEIN; EVALUATION STUDIES AS TOPIC; EVOLUTION, MOLECULAR; GENE EXPRESSION PROFILING; GENOME; HUMANS; PROTEINS; REPRODUCIBILITY OF RESULTS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SEQUENCE ANALYSIS, PROTEIN; SEQUENCE HOMOLOGY, NUCLEIC ACID; SOFTWARE;

EID: 28544451130     PISSN: 14712105     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-6-278     Document Type: Article

References (58)

1. Pevsner J: Bioinformatics and Functional Genomics. Hoboken, NJ: Wiley; 2003.
2. Briffeuil. P, Baudoux G, Lambert C, De Bolle X, Vinals C, Feytmans E, Depiereux E: Comparative analysis of seven multiple protein sequence alignment servers: Clues to enhances reliability of predictions. Bioinformatics 1998, 14(4):357-366.
3. Thompson JD, Plewniak F, Poch O: A comprehensive comparison of multiple sequence alignment programs. Nucleic Acids Res 1999, 27(13):2682-2690.
4. Duret L, Abdeddaim S: Multiple alignments for structrual, functional, or phylogenetic analyses of homologous sequences. In: Bioinformatics: Sequence, Structure, and Databanks. Edited by Higgins D, Taylor W. Oxford: Oxford University Press; 2000: 51-76.
5. Altschul SF, Gish W: Local alignment statistics. In: Methods in Enzymology: Computer Methods for Macromolecular Sequence Analysis. Edited by Doolittle RF, vol. 266. San Diego: Academic Press; 1996: 460-480.
6. Rosenberg MS: Evolutionary distance estimation and fidelity of pair wise sequence alignment. BMC Bioinformatics 2005, 6:102.
7. Pollard DA, Bergman CM, Stoye J, Celniker SE, Eisen MB: Benchmarking tools for the alignment of functional noncoding DNA. BMC Bioinformatics 2004, 5(1):6.
8. Frith MC, Hansen U, Spouge JL, Weng Z: Finding functional sequence elements by multiple local alignment. Nucleic Acids Res 2004, 32(1):189-200.
9. Margulies EH, Blanchette M, Haussler D, Green ED: Identification and characterization of multi-species conserved sequences. Genome Res 2003, 13(12):2507-2518.
10. Xia XH, Xie Z, Kjer KM: 18S ribosomal RNA and tetrapod phylogeny. Syst Biol 2003, 52(3):283-295.
11. Cammarano P, Creti R, Sanangelantoni AM, Palm P: The Archaea monophyly issue: A phylogeny of translational elongation factor G(2) sequences inferred from an optimized selection of alignment positions. J Mol Evol 1999, 49(4):524-537.
12. Kjer KM: Aligned 18S and insect phylogeny. Syst Biol 2004, 53(3):506-514.
13. Kjer KM: Use of rRNA secondary structure in phylogenetic studies to identify homologous positions: An example of alignment and data presentation from the frogs. Mol Phyl Evol 1995, 4(3):314-330.
14. Titus T, Frost DR: Molecular homology assessment and phylogeny in the lizard family Opluridae (Squamata: Iguania). Mol Phyl Evol 1996, 6:49-62.
15. Morrison DA, Ellis JT: Effects of nucleotide sequence alignment on phylogeny estimation: A case study of 18S rDNAs of Acpiocomplexa. Mol Biol Evol 1997, 14:428-441.
16. Hwang UW, Kiim W, Tautz D, Friedrich M: Molecular phylogenetics at the Felsenstein zone: Approaching the Strepsipera probelm using 5.8S and 28S rDNA sequences. Mol Phyl Evol 1998, 9:470-480.
17. Feng DF, Doolittle RF: Progressive alignment and phylogenetic tree constrution of protein sequences. Methods in Enzymology 1990, 183:375-387.
18. Feng DF, Doolittle RF: Progressive sequence alignment as a prerequisite to correct phylogenetic trees. J Mol Evol 1987, 25:351-360.
19. Raghava GPS, Searle SMJ, Audley PC, Barber JD, Barton GJ: OXBench: A benchmark for evaluation of protein multiple sequence alignment accuracy. BMC Bioinformatics 2003, 4:47.
20. Thompson JD, Plewniak F, Poch O: BaliBASE: A benchmarch alignment database for the evaluation of multiple sequence alignment programs. Bioinformatics 1999, 1:87-88.
21. Rosenberg MS, Kumar S: Taxon sampling, bioinformatics, and phylogenomics. Syst Biol 2003, 52(1):119-124.
22. Rosenberg MS, Kumar S: Incomplete taxon sampling is not a problem for phylogenetic inference. PNAS 2001, 98(19):10751-10756.
23. Pollock DD, Zwickl DJ, McGuire JA, Hillis DM: Increased taxon sampling is advantageous for phylogenetic inference. Syst Biol 2002, 51(4):664-671.
24. Zwickl DJ, Hillis DM: Increased taxon sampling greatly reduces phylogenetic error. Syst Biol 2002, 51(4):588-598.
25. Kim J: General inconsistency conditions for maximum parsimony: Effects of branch lengths and increasing numbers of taxa. Syst Biol 1996, 45(3):363-374.
26. Kim J: Large-scale phylogenies and measuring the performance of phylogenetic estimators. Syst Biol 1998, 47(1):43-60.
27. Hendy MD, Penny D: A framework for the quantitative study of evolutionary trees. Syst Zool 1989, 38(4):297-309.
28. Graybeal A: Is it better to add taxa or characters to a difficult phylogenetic problem? Syst Biol 1998, 47(1):9-17.
29. Poe S, Swofford DL: Taxon sampling revisited. Nature 1999, 398(6725):299-300.
30. Fleißner R: Sequence alignment and phylogenetic inference. PhD Thesis. Düsseldorf: Heinrich-Heine-Universität Düsseldorf; 2003.
31. Murphy WJ, Eizirik E, Johnson WE, Zhang YP, Ryder OA, O'Brien SJ: Molecular phylogenetics and the origins of placental mammals. Nature 2001, 409:614-618.
32. Murphy WJ, Eizirik E, O'Brien SJ, Madsen O, Scally M, Douady CJ, Teeling E, Ryder OA, Stanhope MJ, de Jong WW et al: Resolution of the early placental mammal radiation using Bayesian phylogenetics. Science 2001, 294(5550):2348-2351.
33. Reyes A, Gissi C, Catzeflis F, Nevo E, Pesole G, Saccone C: Congruent mammalian trees from mitochondrial and nuclear genes using Bayesian methods. Mol Biol Evol 2004, 21(2):397-403.
34. Gibbs RA, Weinstock GM, Metzker ML, Muzny DM, Sodergren EJ, Scherer S, Scott G, Steffen D, Worley KC, Burch PE et al: Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature 2004, 428(6982):493-521.
35. Hickson RE, Simon C, Perrey SW: The performance of several multiple-sequence alignment programs in relation to secondary-structure features for an rRNA sequence. Mol Biol Evol 2000, 17(4):530-539.
36. Notredame C, Higgins DG, Heringa J: T-Coffee: A novel method for fast and accurate multiple sequence alignment. J Mol Biol 2000, 302(1):205-217.
37. Keightley PD, Johnson T: MCALIGN: Stochastic alignment of noncoding DNA sequences based on an evolutionary model of sequence evolution. Genome Res 2004, 14(3):442-450.
38. Holmes I, Bruno WJ: Evolutionary HMMs: A Bayesian approach to multiple alignment. Bioinformatics 2001, 17(9):803-820.
39. Thorne JL, Kishino H, Felsenstein J: Inching toward reality: An improved likelihood model of sequence evolution. J Mol Evol 1992, 34:3-16.
40. Thorne JL, Kishino H, Felsenstein J: An evolutionary model for maximul likelihood alignment of DNA sequences. J Mol Evol 1991, 33:114-124.
41. Metzler D, Fleißner R, Wakolbinger A, von Haeseler A: Assessing variability by joint sampling of alignments and mutation rates. J Mol Evol 2001, 53:660-669.
42. Hein J, Wiuf C, Knudsen B, Møoller MB, Wibling G: Statistical alignment: Computational properties, homology testing and goodness-of-fit. J Mol Biol 2000, 302:265-279.
43. Fleißner R, Metzler D, von Haeseler A: Can one estimate distances from pairwise sequence alignments? In: Proceedings of the German Conference on Bioinformatics. Edited by Bornberg-Bauer E, Rost U, Stoye J, Vingron M. Berlin: Logos Verlag; 2000: 89-95.
44. Gladstein D, Wheeler WC: POY: The Optimization of Alignment Characters. New York: American Museum of Natural History; 1997.
45. Wheeler WC, Gladstein D: POY: The Optimization of Alignment Characters. New York: American Museum of Natural History; 2000.
46. Redelings BD, Suchard MA: Joint Bayesian estimation of alignment and phylogeny. Syst Biol In press.
47. Lunter G, Miklos I, Drummond A, Jensen JL, Hein J: Bayesian coestimation of phylogeny and sequence alignment. BMC Bioinformatics 2005, 6:83.
48. Fleissner R, Metzler D, von Haeseler A: Simultaneous statistical multiple alignment and phylogeny reconstruction. Syst Biol 2005, 54(4):548-561.
49. Rosenberg MS: MySSP: Non-stationary evolutionary sequence simulation, including indels. Evolutionary Bioinformatics Online 2005, 1:51-53.
50. Hasegawa M, Kishino H, Yano T: Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol 1985, 22:160-174.
51. Rosenberg MS, Subramanian S, Kumar S: Patterns of transitional mutation biases within and among mammalian genomes. Mol Biol Evol 2003, 20(6):988-993.
52. Ophir R, Graur D: Patterns and rates of indel evolution in processed pseudogenes from humans and murids. Gene 1997, 205(1-2):191-202.
53. Sundström H, Webster MT, Ellegren H: Is the rate of insertion and deletion mutation male baised?: Molecular evolutionary analysis of avian and primate sex chromosome sequences. Genetics 2003, 164:259-268.
54. Thompson JD, Higgins DG, Gibson TJ: CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994, 22:4673-4680.
55. Morgenstern B: DIALIGN 2: Improvement of the segment-to-segment approach to multiple sequence alignment. Bioinformatics 1999, 15(3):211-218.
56. Bray N, Dubchak I, Pachter L: AVID: A global alignment program. Genome Res 2003, 13(1):97-102.
57. Brudno M, Do CB, Cooper GM, Kim MF, Davydov E, Green ED, Sidow A, Batzoglou S: LAGAN and Multi-LAGAN: Efficient tools for large-scale multiple alignment of genomic DNA. Genome Res 2003, 13(4):721-731.
58. Tamura K, Nei M: Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 1993, 10:512-526.