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Bioinformatics for Beginners
Genes, Genomes, Molecular Evolution, Databases and Analytical Tools
1st Edition - May 9, 2014
Author: Supratim Choudhuri
Language: English
Hardback ISBN:9780124104716
9 7 8 - 0 - 1 2 - 4 1 0 4 7 1 - 6
eBook ISBN:9780124105102
9 7 8 - 0 - 1 2 - 4 1 0 5 1 0 - 2
Bioinformatics for Beginners: Genes, Genomes, Molecular Evolution, Databases and Analytical Tools provides a coherent and friendly treatment of bioinformatics for any student o…Read more
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Bioinformatics for Beginners: Genes, Genomes, Molecular Evolution, Databases and Analytical Tools provides a coherent and friendly treatment of bioinformatics for any student or scientist within biology who has not routinely performed bioinformatic analysis.
The book discusses the relevant principles needed to understand the theoretical underpinnings of bioinformatic analysis and demonstrates, with examples, targeted analysis using freely available web-based software and publicly available databases. Eschewing non-essential information, the work focuses on principles and hands-on analysis, also pointing to further study options.
Avoids non-essential coverage, yet fully describes the field for beginners
Explains the molecular basis of evolution to place bioinformatic analysis in biological context
Provides useful links to the vast resource of publicly available bioinformatic databases and analysis tools
Contains over 100 figures that aid in concept discovery and illustration
Graduate students and researchers in molecular biology, genetics and bioinformatics, and across biology disciplines
Dedication
Preface
Acknowledgment
Chapter 1. Fundamentals of Genes and Genomes
1.1 Biological Macromolecules, Genomics, and Bioinformatics
1.2 DNA as the Universal Genetic Material
1.3 DNA Double Helix
1.4 Conformations of DNA
1.5 Typical Eukaryotic Gene Structure
1.6 Mutations in the DNA Sequence
1.7 Some Features of RNA
1.8 Coding Versus Noncoding RNA
1.9 Protein Structure and Function
1.10 Genome Structure and Organization
References
Chapter 2. Fundamentals of Molecular Evolution
2.1 Bioinformatics, Molecular Evolution, and Phylogenetics
2.2 Biological Evolution and Basic Premises of Darwinism
2.3 Molecular Basis of Heritable Genetic Variations—The Raw Materials for Evolution
2.4 Factors that Affect Gene Frequency in a Population
2.5 The Neutral Theory of Evolution
2.6 Molecular Clock Hypothesis in Molecular Evolution
2.7 Molecular Phylogenetics
References
Chapter 3. Genomic Technologies
3.1 Advances in Genomics
3.2 From Sanger Sequencing to Pyrosequencing
3.3 Pyrosequencing, Mutation Detection, and SNP Genotyping
3.4 Next-Generation Sequencing Platforms
3.5 Next-next-generation Sequencing Technology
3.6 High-Density Oligonucleotide-Probe-based Array to Investigate Genome Expression
3.7 Genome-Wide Mutagenesis, Genome Editing, and Interference of Genome Expression
3.8 Special Topic: Optical Mapping of DNA
References
Chapter 4. The Beginning of Bioinformatics
4.1 Margaret Dayhoff, Richard Eck, Robert Ledley, and the Beginning of Bioinfomatics
4.2 Definition of Bioinformatics
4.3 Bioinformatics Versus Computational Biology
4.4 Goals of Bioinformatic Analysis
4.5 Bioinformatics Technical Toolbox
References
Chapter 5. Data, Databases, Data Format, Database Search, Data Retrieval Systems, and Genome Browsers
5.1 Genomic Data
5.2 Sequence Data Formats
5.3 Conversion of Sequence Formats Using Readseq
5.4 Primary Sequence Databases—GenBank, EMBL-Bank, and DDBJ
5.5 Secondary Databases
5.6 Some Examples of Publicly Available Secondary and Specialized Databases
5.7 Data Retrieval
5.8 An Example of Retrieval of mRNA/Gene Information
5.9 Data Visualization in Genome Browsers
5.10 Using Map Viewer to Search the Genome
5.11 A Note on the State of the Sequence-Assembly Data in Different Databases
References
Chapter 6. Sequence Alignment and Similarity Searching in Genomic Databases: BLAST and FASTA
6.1 Evolutionary Basis of Sequence Alignment
6.2 Three Terms—Sequence Identity, Sequence Similarity, and Sequence Homology—And Their Proper Usage
6.3 Sequence Identity and Sequence Similarity
6.4 Global Versus Local Alignment
6.5 Pairwise and Multiple Alignment
6.6 Alignment Algorithms, Gaps, and Gap Penalties
6.7 Scoring Matrix, Alignment Score, and Statistical Significance of Sequence Alignment
6.8 Database Searching with the Heuristic Versions of the Smith–Waterman Algorithm—BLAST and FASTA
6.9 Sequence Comparison, Synteny, and Molecular Evolution
7.4 Prediction of Promoters, Transcription-Factor-Binding Sites, Translation Initiation Sites, and the ORF
7.5 Restriction-Site Mapping of the Input Sequence
7.6 RNA Secondary-Structure Prediction
7.7 Microarray Analysis
7.8 Detection of Sequence Polymorphism and the SNP Database
References
Chapter 8. Additional Bioinformatic Analyses Involving Protein Sequences
8.1 Protein Structure
8.2 Peptide Bond, Peptide Plane, Bond Rotation, Dihedral Angles, and Ramachandran Plot
8.3 Prediction of Physicochemical Properties of a Protein
8.4 Prediction of Protease Digestibility
8.5 Hydrophobicity, Hydrophilicity, and Antigenicity Prediction, and the Hydropathy Plot
8.6 Prediction of Post-Translational Modification and Sorting
8.7 Secondary-Structure Prediction
8.8 Prediction of Domains and Motifs
8.9 Viewing the 3D Structure of Proteins (And Other Biological Macromolecules)
8.10 Allergenic Protein Databases and Protein-Allergenicity Prediction
8.11 Intrinsically Disordered Protein Analysis
References
Chapter 9. Phylogenetic Analysis
9.1 Phylogenetics and the Widespread Use of the Phylogenetic Tree
9.2 Phylogenetic Trees
9.3 Phylogenetic Analysis Tools
9.4 Principles of Phylogenetic-Tree Construction
9.5 Monophyly, Polyphyly, and Paraphyly
9.6 Species Trees Versus Gene Trees
References
Index
No. of pages: 238
Language: English
Edition: 1
Published: May 9, 2014
Imprint: Academic Press
Hardback ISBN: 9780124104716
eBook ISBN: 9780124105102
SC
Supratim Choudhuri
Dr. Supratim Choudhuri is a toxicologist at the Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration. Dr. Choudhuri has extensively published in the fields of molecular toxicology, metabolism, genomics, and epigenetics. He has previously edited a book, titled Genomics: Fundamentals and Applications with a colleague Dr. David B. Carlson.
Affiliations and expertise
Division of Biotechnology and GRAS Notice Review, Office of Food Additive Safety, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration