Non-negative matrix factorization for learning alignment-specific models of protein evolution

PLoS ONE

Volumn 6, Issue 12, 2011, Pages

  Murrell, Ben ^a,b   Weighill, Thomas ^b   Buys, Jan ^b   Ketteringham, Robert ^b   Moola, Sasha ^c   Benade, Gerdus ^b   Buisson, Lise ^b   Kaliski, Daniel ^c   Hands, Tristan ^c   Scheffler, Konrad ^b  

^a SOUTH AFRICAN MEDICAL RESEARCH COUNCIL   (South Africa)

^b STELLENBOSCH UNIVERSITY   (South Africa)

^c UNIVERSITY OF CAPE TOWN   (South Africa)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; BIOINFORMATICS; CONTROLLED STUDY; DATA PROCESSING; GENETIC CONSERVATION; LEARNING; NON NEGATIVE MATRIX FACTORIZATION; PHYLOGENY; PROTEIN ALIGNMENT; PROTEIN EVOLUTION; PROTEIN PROCESSING; QUANTITATIVE ANALYSIS; SEQUENCE ANALYSIS; STATISTICAL ANALYSIS; EVOLUTION; PHYSIOLOGY; THEORETICAL MODEL;

PROTEIN;

BIOLOGICAL EVOLUTION; MODELS, THEORETICAL; PHYLOGENY; PROTEINS;

EID: 84055216948     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0028898     Document Type: Article

References (33)

1. Dayhoff MO, Eck RV, Park CM, (1972) A model of evolutionary change in proteins. In: Dayhoff M, editors. pp. 89-99 Atlas of Protein Sequence and Structure, National Biomedical Research Foundation, Washington, D.C., volume 5.
2. Dayhoff MO, Schwartz RM, Orcutt BC, (1978) A model of evolutionary change in proteins. In: Dayhoff M, editors. pp. 345-352 Atlas of Protein Sequence and Structure, National Biomedical Research Foundation, Washington, D.C., volume 5, suppl. 3.
3. Lipman DJ, Altschul SF, Kececioglu JD, (1989) A tool for multiple sequence alignment. Proceedings of the National Academy of Sciences of the United States of America 86: 4412-4415.
4. Felsenstein J, (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. Journal of molecular evolution 17: 368-376.
5. Kosakovsky Pond SL, Poon AF, Leigh Brown AJ, Frost SD, (2008) A maximum likelihood method for detecting directional evolution in protein sequences and its application to inuenza A virus. Mol Biol Evol 25: 1809-1824.
6. Jones DT, Taylor WR, Thornton JM, (1992) The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci 8: 275-282.
7. Kosiol C, Goldman N, (2005) Different Versions of the Dayhoff Rate Matrix. Molecular Biology and Evolution 22: 193-199.
8. Whelan S, Goldman N, (2001) A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Mol Biol Evol 18: 691-699.
9. Adachi J, Hasegawa M, (1996) Model of amino acid substitution in proteins encoded by mitochondrial DNA. Journal of molecular evolution 42: 459-468.
10. Yang Z, Nielsen R, Hasegawa M, (1998) Models of amino acid substitution and applications to mitochondrial protein evolution. Mol Biol Evol 15: 1600-1611.
11. Cao Y, Waddell PJ, Okada N, Hasegawa M, (1998) The complete mitochondrial DNA sequence of the shark Mustelus manazo: evaluating rooting contradictions to living bony vertebrates. Mol Biol Evol 15: 1637-1646.
12. Dimmic MW, Rest JS, Mindell DP, Goldstein RA, (2002) rtREV: an amino acid substitution matrix for inference of retrovirus and reverse transcriptase phylogeny. Journal of molecular evolution 55: 65-73.
13. Nickle DC, Heath L, Jensen MA, Gilbert PB, Mullins JI, et al. (2007) HIV-Specific Probabilistic Models of Protein Evolution. PLoS ONE 2: e503+.
14. Lee DD, Seung HS, (1999) Learning the parts of objects by non-negative matrix factorization. Nature 401: 788-791.
15. Devarajan K, (2008) Nonnegative Matrix Factorization: An Analytical and Interpretive Tool in Computational Biology. PLoS Comput Biol 4: e1000029+.
16. Abascal F, Zardoya R, Posada D, (2005) ProtTest: selection of best-fit models of protein evolution. Bioinformatics 21: 2104-2105.
17. Kosakovsky Pond SL, Frost SDW, Muse SV, (2005) HyPhy: hypothesis testing using phylogenies. Bioinformatics 21: 676-679.
18. Yang Z, (2007) PAML 4: Phylogenetic Analysis by Maximum Likelihood. Mol Biol Evol 24: 1586-1591.
19. Guindon SA, Dufayard JFA, Lefort V, Anisimova M, Hordijk W, et al. (2010) New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0. Systematic Biology 59: 307-321.
20. Burnham KP, Anderson D, (2002) Model Selection and Multi-Model Inference Springer, 2nd edition.
21. Posada D, Buckley TR, (2004) Model Selection and Model Averaging in Phylogenetics: Advantages of Akaike Information Criterion and Bayesian Approaches Over Likelihood Ratio Tests. Systematic biology 53: 793-808.
22. Robinson D, (1981) Comparison of phylogenetic trees. Mathematical Biosciences 53: 131-147.
23. Felsenstein J, (1989) PHYLIP- Phylogeny Inference Package (Version 3.2). Cladistics 5: 164-166.
24. Whelan S, de Bakker PIW, Quevillon E, Rodriguez N, Goldman N, (2006) PANDIT: an evolution- centric database of protein and associated nucleotide domains with inferred trees. Nucleic Acids Research 34: D327-D331.
25. Stanfel L, (1996) A New Approach to Clustering the Amino Acid. Journal of Theoretical Biology 183: 195-205.
26. Delport W, Scheffler K, Botha G, Gravenor MB, Muse SV, et al. (2010) CodonTest: Modeling Amino Acid Substitution Preferences in Coding Sequences. PLoS Comput Biol 6: e1000885+.
27. Burnham KP, Anderson DR, (2004) Multimodel Inference. Sociological Methods & Research 33: 261-304.
28. Posada D, Crandall KA, (1998) MODELTEST: testing the model of DNA substitution. Bioinformatics (Oxford, England) 14: 817-818.
29. Zoller S, Schneider A, (2011) A new semi-empirical codon substitution model based on principal component analysis of Mammalian sequences. Mol Biol Evol Advance access.
30. Goldman N, Thorne JL, Jones DT, (1998) Assessing the Impact of Secondary Structure and Solvent Accessibility on Protein Evolution. Genetics 149: 445-458.
31. Lartillot N, Philippe H, (2004) A Bayesian Mixture Model for Across-Site Heterogeneities in the Amino-Acid Replacement Process. Molecular Biology and Evolution 21: 1095-1109.
32. Le SQ, Lartillot N, Gascuel O, (2008) Phylogenetic mixture models for proteins. Philosophical Transactions of the Royal Society B: Biological Sciences 363: 3965-3976.
33. Le SQ, Gascuel O, (2010) Accounting for Solvent Accessibility and Secondary Structure in Protein Phylogenetics Is Clearly Beneficial. Systematic Biology 59: 277-287.