Title Page
by Mir Asif Iquebal, Ratan Kumar Choudhary, Chandra Sekhar Mukhopadhyay
Basic Applied Bioinformatics
- Cover
- Title Page
- Preface
- Acknowledgments
- List of Abbreviations
- SECTION I: Molecular Sequences and Structures
- CHAPTER 1: Retrieval of Sequence(s) from the NCBI Nucleotide Database
- CHAPTER 2: Retrieval of Protein Sequence from UniProtKB
- CHAPTER 3: Downloading Protein Structure
- CHAPTER 4: Visualizing Protein Structure
- CHAPTER 5: Sequence Format Conversion
- CHAPTER 6: Nucleotide Sequence Analysis Using Sequence Manipulation Suite (SMS)
- CHAPTER 7: Detection of Restriction Enzyme Sites
- SECTION II: Sequence Alignment
- SECTION III: Basic Local Alignment Search Tools
- SECTION IV: Primer Designing and Quality Checking
- SECTION V: Molecular Phylogenetics
- CHAPTER 21: Construction of Phylogenetic Tree: Unweighted‐Pair Group Method with Arithmetic Mean (UPGMA)
- CHAPTER 22: Construction of Phylogenetic Tree: Fitch Margoliash (FM) Algorithm
- CHAPTER 23: Construction of Phylogenetic Tree: Neighbor‐Joining Method
- CHAPTER 24: Construction of Phylogenetic Tree: Maximum Parsimony Method
- CHAPTER 25: Construction of Phylogenetic Tree: Minimum Evolution Method
- CHAPTER 26: Construction of Phylogenetic Tree Using MEGA7
- CHAPTER 27: Interpretation of Phylogenetic Trees
- SECTION VI: Protein Structure Prediction
- CHAPTER 28: Prediction of Secondary Structure of Protein
- CHAPTER 29: Prediction of Tertiary Structure of Protein: Sequence Homology
- CHAPTER 30: Protein Structure Prediction Using Threading Method
- CHAPTER 31: Prediction of Tertiary Structure of Protein: Ab Initio Approach
- CHAPTER 32: Validation of Predicted Tertiary Structure of Protein
- SECTION VII: Molecular Docking and Binding Site Prediction
- SECTION VIII: Genome Annotation
- SECTION IX: Advanced Biocomputational Analyses
- CHAPTER 38: Concepts of Real‐Time PCR Data Analysis
- CHAPTER 39: Overview of Microarray Data Analysis
- 39.1 CONCEPT
- 39.2 GETTING STARTED WITH MICROARRAY
- 39.3 MICROARRAY DATA ANALYSIS: GENE EXPRESSION ANALYSIS
- 39.4 STEPS INVOLVED IN MICROARRAY DATA ANALYSIS
- 39.5 FUNCTIONAL INFORMATION USING GENE NETWORKS AND PATHWAYS
- 39.6 LIVESTOCK RESEARCH THAT INVOLVED MICROARRAY ANALYSIS (SOME EXAMPLES)
- 39.7 APPLICATIONS OF MICROARRAY
- 39.8 QUESTIONS
- CHAPTER 40: Single Nucleotide Polymorphism (SNP) Mining Tools
- CHAPTER 41: In Silico Mining of Simple Sequence Repeats (SSR) Markers
- CHAPTER 42: Basics of RNA‐Seq Data Analysis
- CHAPTER 43: Functional Annotation of Common Differentially Expressed Genes
- CHAPTER 44: Identification of Differentially Expressed Genes (DEGs)
- 44.1 SECTION I. QUALITY FILTERING OF DATA USING PRINSEQ
- 44.2 SECTION II. IDENTIFICATION OF DIFFERENTIALLY EXPRESSED GENES – I (USING CUFFLINKS)
- 44.3 SECTION III. IDENTIFICATION OF DIFFERENTIALLY EXPRESSED GENES – II (USING RSEM‐DE PACKAGES EBSEQ, DESEQ2 AND EDGER)
- 44.4 USE OF DE PACKAGES FOR IDENTIFYING THE DIFFERENTIALLY EXPRESSED GENES
- 44.5 QUESTIONS
- CHAPTER 45: Estimating MicroRNA Expression Using the miRDeep2 Tool
- CHAPTER 46: miRNA Target Prediction
- 46.1 INTRODUCTION
- 46.2 miRNA TARGET PREDICTION BY TARGETSCAN (http://targetscan.org/)
- 46.3 miRNA TARGET PREDICTION BY TARGETSCAN IN HUMAN
- 46.4 miRNA TARGET PREDICTION BY psRNATARGET (http://plantgrn.noble.org/psRNATarget>/)
- 46.5 miRNA TARGET PREDICTION BY miRANDA (http://www.microrna.org)
- 46.6 QUESTIONS
- Appendix A: Usage of Internet for Bioinformatics
- Appendix B: Important Web Resources for Bioinformatics Databases and Tools
- Appendix C: NCBI Database: A Brief Account
- Appendix D: EMBL Databases and Tools: An Overview
- Appendix E: Basics of Molecular Phylogeny
- Appendix F: Evolutionary Models of Molecular Phylogeny
- Glossary
- References
- Webliography
- Index
- End User License Agreement
Basic Applied Bioinformatics
Chandra Sekhar Mukhopadhyay
Ratan Kumar Choudhary
Mir Asif Iquebal
With contributions from
Ravi GVPPS Kumar, Sarika, Dinesh Kumar, Aditya Prasad Sahoo, Amit Kumar, Saurabh Jain, Surbhi Panwar, Ashwani Kumar, Harpreet Kaur Manku
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