SECTION III: Basic Local Alignment Search Tools
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
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