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• Cover
• Foreword
• Preface
• Contributors
• About the Companion Website
• 1 Biological Sequence Databases
• Introduction
• Nucleotide Sequence Databases
• Nucleotide Sequence Flatfiles: A Dissection
• Protein Sequence Databases
• Summary
• Acknowledgments
• Internet Resources
• Further Reading
• References
• 2 Information Retrieval from Biological Databases
• Introduction
• Integrated Information Retrieval: The Entrez System
• Medical Databases
• Organismal Sequence Databases Beyond NCBI
• Summary
• Further Reading
• References
• 3 Assessing Pairwise Sequence Similarity: BLAST and FASTA
• Introduction
• Global Versus Local Sequence Alignments
• Scoring Matrices
• BLAST
• BLAST 2 Sequences
• MegaBLAST
• PSI-BLAST
• BLAT
• FASTA
• Summary
• Further Reading
• References
• 4 Genome Browsers
• Introduction
• The UCSC Genome Browser
• UCSC Table Browser
• ENSEMBL Genome Browser
• Ensembl Biomart
• JBrowse
• Summary
• Further Reading
• References
• 5 Genome Annotation
• Introduction
• Gene Prediction Methods
• Ab Initio Gene Prediction in Prokaryotic Genomes
• Ab Initio Gene Prediction in Eukaryotic Genomes
• How Well Do Gene Predictors Work?
• Assessing Prokaryotic Gene Predictors
• Assessing Eukaryotic Gene Predictors
• Evidence Generation for Genome Annotation
• Gene Annotation and Evidence Generation using Comparative Gene Prediction
• Genome Annotation Pipelines
• Summary
• Acknowledgments
• Internet Resources
• Further Reading
• References
• 6 Predictive Methods Using RNA Sequences
• Introduction
• Overview of RNA Secondary Structure Prediction Using Thermodynamics
• Dynamic Programming
• Accuracy of RNA Secondary Structure Prediction
• Predicting the Secondary Structure Common to Multiple RNA Sequences
• Practical Introduction to Single-Sequence Methods
• Practical Introduction to Multiple Sequence Methods
• Other Computational Methods to Study RNA Structure
• Comparison of Methods
• Predicting RNA Tertiary Structure
• Summary
• Further Reading
• References
• 7 Predictive Methods Using Protein Sequences
• Introduction
• One-Dimensional Prediction of Protein Structure
• Predicting Protein Function
• Summary
• Further Reading
• References
• 8 Multiple Sequence Alignments
• Introduction
• Measuring Multiple Alignment Quality
• Making an Alignment: Practical Issues
• Commonly Used Alignment Packages
• Viewing a Multiple Alignment
• Summary
• References
• 9 Molecular Evolution and Phylogenetic Analysis
• Introduction
• Early Classification Schemes
• Sequences As Molecular Clocks
• Background Terminology and the Basics
• How to Construct a Tree
• Marker-Based Evolution Studies
• Phylogenetic Analysis and Data Integration
• Future Challenges
• References
• 10 Expression Analysis
• Introduction
• Step 0: Choose an Expression Analysis Technology
• Step 1: Design the Experiment
• Step 2: Collect and Manage the Data – and Metadata
• Step 3: Data Pre-Processing
• Step 4: Quality Control
• Step 5: Normalization and Batch Effects
• Step 6: Exploratory Data Analysis
• Step 7: Differential Expression Analysis
• Step 8: Exploring Mechanisms Through Functional Enrichment Analysis
• Step 9: Developing a Classifier
• Single-Cell Sequencing
• Summary
• Further Reading
• References
• 11 Proteomics and Protein Identification by Mass Spectrometry
• Introduction
• Mass Spectrometry
• Tandem Mass Spectrometry for Peptide Identification
• Sample Preparation
• Bioinformatics Analysis for MS-based Proteomics
• Proteomics Strategies
• Peptide Mass Fingerprinting
• PMF on the Web
• Proteomics and Tandem MS
• PSM Software
• PSM on the Web
• Reporting Standards
• Proteomics Data Repositories
• Protein/Proteomics Databases
• Selected Applications of Proteomics
• Summary
• Acknowledgments
• Internet Resources
• Further Reading
• References
• 12 Protein Structure Prediction and Analysis
• Introduction to Protein Structures
• How Protein Structures are Determined
• How Protein Structures are Described
• Protein Structure Databases
• Visualizing Proteins
• Protein Structure Prediction
• Protein Structure Evaluation
• Protein Structure Comparison
• Summary
• Further Reading
• References
• 13 Biological Networks and Pathways
• Introduction
• Pathway and Molecular Interaction Mapping: Experiments and Predictions
• Pathway and Molecular Interaction Databases: An Overview
• Pathway Databases
• Molecular Interaction Databases
• Functional Interaction Databases
• Strategies for Navigating Pathway and Interaction Databases
• Standard Data Formats for Pathways and Molecular Interactions
• Pathway Visualization and Analysis
• Network Visualization and Analysis
• Summary
• Acknowledgments
• Internet Resources
• Further Reading
• References
• 14 Metabolomics
• Introduction
• Data Formats
• Databases
• Bioinformatics for Metabolite Identification
• Multivariate Statistics
• Bioinformatics for Metabolite Interpretation
• Summary
• Further Reading
• References
• 15 Population Genetics
• Introduction
• Evolutionary Processes and Genetic Variation
• Allele Frequencies and Population Variation
• Display Methods
• Demographic History Inference
• Admixture and Ancestry Estimation
• Detection of Natural Selection
• Other Applications
• Summary
• References
• 16 Metagenomics and Microbial Community Analysis
• Introduction
• Why Study the Microbiome?
• The Origins of Microbiome Analysis
• Metagenomic Workflow
• General Considerations in Marker-Gene and Metagenomic Data Analysis
• Marker Genes
• Metagenomic Data Analysis
• Other Techniques to Characterize the Microbiome
• Summary
• Further Reading
• References
• 17 Translational Bioinformatics
• Introduction
• Databases Describing the Genetics of Human Health
• Prediction and Characterization of Impactful Genetic Variants from Sequence
• Computing with Patient Phenotype Using Data in Electronic Health Records
• Informatics and Precision Medicine
• Ethical, Legal, and Social Implications of Translational Medicine
• Summary
• References
• 18 Statistical Methods for Biologists
• Introduction
• Descriptive Representations of Data
• Statistical Inference and Statistical Hypothesis Testing
• Summary
• Acknowledgments
• Internet Resources
• Further Reading
• References
• Appendices
• 1.1 Example of a Flatfile Header in ENA Format
• 1.2 Example of a Flatfile Header in DDBJ/GenBank Format
• 1.3 Example of a Feature Table in ENA Format
• 1.4 Example of a Feature Table in GenBank/DDBJ Format
• 6.1 Dynamic Programming
• Reference
• Glossary
• Index
• End User License Agreement