PART Ⅰ DATABASES AND BIOINFORMATICS TOOLS Chapter 1 Online Sequence Database 1.1 Nucleic Acid Sequence Database 1.2 Protein Database 1.3 Protein Three-Dimensional Structure Database PDB 1.4 Genome Browser References Chapter 2 Sequence Alignment 2.1 Pairwise Sequence Alignment 2.2 Multiple Sequence Alignment 2.3 Basic Local Alignment Search Tool References Chapter 3 Molecular Phylogeny and Evolution 3.1 Introduction to Molecular Evolution 3.2 Models of DNA and Amino Acid Substitution 3.3 Tree-Building Method 3.4 Evaluating Tree 3.5 Perspectives References Chapter 4 Predicting DNA and Protein Function from Sequence 4.1 DNA Sequence Analysis 4.2 Protein Sequence Analysis References Chapter 5 Protein Structure 5.1 Overview of Protein Structure 5.2 Principles of Protein Structure 5.3 Protein Structure Prediction 5.4 Protein Structure Determining and Analysis References PART Ⅱ BIOINFORMATICS FOR OMICS DATA Chapter 6 Human Genetic Variation and Human Disease 6.1 Human Genetic Variation 6.2 Human Disease References Chapter 7 Gene Expression Profiling with Microarray: Online Resources and Data Management 7.1 Microarray Data Analysis Software 7.2 Microarray Databases 7.3 Microarray Data Analysis References Chapter 8 Bioinformatics for Qualitative and Quantitative Proteomics 8.1 Protein Identification and Quantification from MS Raw Data 8.2 Proteomics Data Analysis 8.3 Proteomics Data Storage, Exchange and Sharing References Chapter 9 Bioinformatics for Metabolomics 9.1 Metabonomics and Metabolomics 9.2 Basic Approaches to Study Metabonomics 9.3 Data Analysis Methods 9.4 Metabonomics Databases 9.5 Summary
References Chapter 10 Gene Ontology Database and KEGG Database 10.1 Gene Ontology Database 10.2 KEGG Database References PART Ⅲ STATISTICS AND PROGRAMMING Chapter 11 Basic Algorithms for Bioinformatics 11.1 Algorithms 11.2 Graph Theory 11.3 Dynamic Programming 11.4 Bayesian Statistics 11.5 Markov Models 11.6 Hidden Markov Model 11.7 Neural Networks 11.8 Clustering Analysis 11.9 Other Algorithms 11.10 Concluding Remarks References Chapter 12 An Introduction to R 12.1 What's R 12.2 How to Install R 12.3 RGui 12.4 How to Install R Extention Packages 12.5 Expressions and Assignments 12.6 Data Structure 12.7 Importing Data Into R 12.8 Exporting Data 12.9 Loops/Statements 12.10 Bioconductor 12.11 Further Resources References Index
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