DSpace at VNU: Protein type specific amino acid substitution models for influenza viruses

Protein type specific amino acid substitution models for influenza viruses Nguyễn Văn Sáu Trường Đại học Công nghệ Luận văn Thạc sĩ ngành: Khoa học máy tính; Mã số: 60 48 01 Người hướng dẫn: TS Lê Sỹ Vinh Năm bảo vệ: 2012 Keywords Khoa học máy tính; Mơ hình liệu; Amino acid; Mơ hình dự tốn Content ACKNOWLEDGMENTS I LIST OF FIGURES LIST OF TABLES NOTATIONS/ABBREVIATIONS ORIGINALITY STATEMENT ABSTRACT CHAPTER OVERVIEW 1.1 Motivation 1.2 Organization of this thesis CHAPTER AMINO ACID SUBSTITUTION MODELS 2.1Amino acid sequences 2.2 Amino-acid substitution models 10 CHAPTER METHODS TO ESTIMATE MODELS 13 4.1 Methods 13 4.1.1 Counting methods 13 4.1.2 Maximum likelihood methods 14 4.2 Protein type specific amino acid substitution models estimation 17 CHAPTER DATA PREPARATION 21 3.1 Collecting data 21 3.2 Categorizing data 23 3.3 Splitting data 27 3.4 Aligning data 28 CHAPTER RESULTS 29 CHAPTER SUMMARY AND CONCLUSION 34 APPENDIX 35 BIBLIOGRAPHY 36 References Adachi, Jun and Hasegawa, Masami, 1996 Model of Amino Acid Substitution in Proteins Encoded by Mitochondrial DNA J Mol Evol., pp 459-468 Bao Y, Bolotov P, Dernovoy D, Kiryutin B, Zaslavsky L, Tatusova T, Ostell J, Lipman D, 2008 The Influenza Virus Resource at the National Center for Biotechnology Information J Virol, Volume 82, pp 596-601 Brown, T., 2002 Genomes Oxford: BIOS Scientific Publishers Ltd Castresana, J., 2000 Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis Molecular Biology and Evolution, Volume 17, pp 540-552 Churchill GA, Haeseler AV, Navidi WC, 1992 Sample Size for Phylogenetic Inference Mol Biol Evol, Volume 9, pp 753-769 Cuong Cao Dang, Quang Si Le, Olivier Gascuel and Vinh Sy Le, 2010 FLU, an amino acid substitution model for influenza proteins BMC Evolutionary Biology, Volume 10, pp 99 D.T Jones, W.R Taylor, J.M Thornton, 1994 A mutation data matrix for transmembrane proteins FEBSLetters, Volume 339, pp 269-275 Daniel A Janies, Andrew Hill, Rob Guralnick, Farhat Habib, Eric Waltari, Ward C Wheeler, 2007 Genomic Analysis and Geographic Visualization of the Spread of Avian Influenza (H5N1) Systematic Biology, Volume 56, pp 321-329 David C Nickle, Laura Heath, Mark A Jensen, Peter B Gilbert, James I Mullins, and Sergei L Kosakovsky Pond, 2007 HIV-Specific Probabilistic Models of Protein Evolution PLoS ONE, Volume 2, pp 503 Dayhoff, M O and Schwartz, R M and Orcutt, B C, 1978 A Model of Evolutionary Change in Proteins In: M O Dayhoff, ed Atlas of Protein Sequence Structure Washington DC: National Biomedical Research Foundation, pp 345-352 Dayhoff, M O., R V ECK, and C M Park, 1972 A model of evolutionary change in proteins National Biomedical Research Foundation, Volume 5, pp 89-99 Dayhoff, 1972 Atlas of Protein Sequence and Structure Washington DC: National Biomedical Research Foundation Edgar, Robert C., 2004 MUSCLE: multiple sequence alignment with high accuracy and high throughput Nucl Acids Res., Volume 32, pp 1792-1797 Fauci, A S., 2009 Race against time Nature, Volume 435 Felsenstein, Joseph, 1984 Distance methods for inferring phylogenies: A Justification Evolution, Volume 38, pp 16-24 Felsenstein, J., 1981 Evolutionary trees from DNA sequences: A maximum likelihood approach Journal of Molecular Evolution, Volume 17, pp 368-376 Felsenstein, J., Massachusetts 2004 Infering Phylogenies Sinauer Associates, Sunderland, Fitch WM, Margoliash E, 1967 A method for estimating the number of invariant amino acid position in a gene using cytochrome c as a model case Biochem Gene, Volume 1, pp 65-71 Gaston H Gonnet, Mark A Cohen, Steven A Benner, 1992 Exhaustive Matching of the Entire Protein Sequence Database Science, Volume 256, pp 1443-1445 Gu X, Fu YX, Li WH, 1995 Maximum Likelihood Estimation of the Heterogeneity of Substitution Rate among Nucleotide Sites Mol Biol Evol, Volume 12, pp 546-557 Henikoff, S.; 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FLU, an amino acid substitution model for influenza proteins BMC Evolutionary Biology, Volume 10, pp 99 D.T Jones, W.R Taylor, J.M Thornton, 1994 A mutation data matrix for transmembrane proteins... Amino Acid Substitution Matrices from Protein Blocks PNAS, Volume 89, pp 10915-10919 Jones, David T and Taylor, William R and Thornton, Janet M., 1992 The rapid generation of mutation data matrices... XRate: a fast prototyping, training and annotation tool for phylo-grammars BMC Bioinformatics, Volume 7, pp 428 Quang Le and Olivier Gascuel, 2008 An improved general amino acid replacement matrix