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Basic Applied Bioinformatics

Book Description

An accessible guide that introduces students in all areas of life sciences to bioinformatics

Basic Applied Bioinformatics provides a practical guidance in bioinformatics and helps students to optimize parameters for data analysis and then to draw accurate conclusions from the results. In addition to parameter optimization, the text will also familiarize students with relevant terminology. Basic Applied Bioinformatics is written as an accessible guide for graduate students studying bioinformatics, biotechnology, and other related sub-disciplines of the life sciences.

This accessible text outlines the basics of bioinformatics, including pertinent information such as downloading molecular sequences (nucleotide and protein) from databases; BLAST analyses; primer designing and its quality checking, multiple sequence alignment (global and local using freely available software); phylogenetic tree construction (using UPGMA, NJ, MP, ME, FM algorithm and MEGA7 suite), prediction of protein structures and genome annotation, RNASeq data analyses and identification of differentially expressed genes and similar advanced bioinformatics analyses. The authors Chandra Sekhar Mukhopadhyay, Ratan Kumar Choudhary, and Mir Asif Iquebal are noted experts in the field and have come together to provide an updated information on bioinformatics.

Salient features of this book includes:

  • Accessible and updated information on bioinformatics tools
  • A practical step-by-step approach to molecular-data analyses
  • Information pertinent to study a variety of disciplines including biotechnology, zoology, bioinformatics and other related fields
  • Worked examples, glossary terms, problems and solutions

Basic Applied Bioinformatics gives students studying bioinformatics, agricultural biotechnology, animal biotechnology, medical biotechnology, microbial biotechnology, and zoology an updated introduction to the growing field of bioinformatics.

Table of Contents

  1. Cover
  2. Title Page
  3. Preface
  4. Acknowledgments
  5. List of Abbreviations
  6. SECTION I: Molecular Sequences and Structures
    1. CHAPTER 1: Retrieval of Sequence(s) from the NCBI Nucleotide Database
      1. 1.1 INTRODUCTION
      2. 1.2 COMPONENTS OF THE NCBI NUCLEOTIDE DATABASE
      3. 1.3 OBJECTIVES
      4. 1.4 PROCEDURE
      5. 1.5 SOME USEFUL NUCLEOTIDE SEQUENCE DATABASES OF NCBI
      6. 1.6 QUESTIONS
    2. CHAPTER 2: Retrieval of Protein Sequence from UniProtKB
      1. 2.1 INTRODUCTION
      2. 2.2 OBJECTIVE
      3. 2.3 PROCEDURE
      4. 2.4 QUESTIONS
    3. CHAPTER 3: Downloading Protein Structure
      1. 3.1 INTRODUCTION
      2. 3.2 OBJECTIVE
      3. 3.3 PROCEDURE
      4. 3.4 QUESTIONS
    4. CHAPTER 4: Visualizing Protein Structure
      1. 4.1 INTRODUCTION
      2. 4.2 OBJECTIVE
      3. 4.3 PROCEDURE
      4. 4.4 QUESTIONS
    5. CHAPTER 5: Sequence Format Conversion
      1. 5.1 INTRODUCTION
      2. 5.2 OBJECTIVE
      3. 5.3 PROCEDURE
      4. 5.4 QUESTIONS
      5. 5.5 BRIEF DESCRIPTION OF SOME OF THE IMPORTANT MOLECULAR SEQUENCE FORMATS
    6. CHAPTER 6: Nucleotide Sequence Analysis Using Sequence Manipulation Suite (SMS)
      1. 6.1 INTRODUCTION
      2. 6.2 OBJECTIVE
      3. 6.3 PROCEDURE
      4. 6.4 FORMAT CONVERSION
      5. 6.5 SEQUENCE ANALYSIS
      6. 6.6 SEQUENCE FIGURES
      7. 6.7 RANDOM SEQUENCES
      8. 6.8 MISCELLANEOUS
      9. 6.9 QUESTIONS
    7. CHAPTER 7: Detection of Restriction Enzyme Sites
      1. 7.1 INTRODUCTION
      2. 7.2 OBJECTIVE
      3. 7.3 PROCEDURE (USING NEBCUTTER)
      4. 7.4 QUESTIONS
  7. SECTION II: Sequence Alignment
    1. CHAPTER 8: Dot Plot Analysis
      1. 8.1 INTRODUCTION
      2. 8.2 OBJECTIVE
      3. 8.3 PROCEDURE
      4. 8.4 PARAMETERS OF DOT PLOT ANALYSIS
      5. 8.5 INTERPRETATION
      6. 8.6 QUESTIONS
    2. CHAPTER 9: Needleman–Wunsch Algorithm (Global Alignment)
      1. 9.1 INTRODUCTION
      2. 9.2 OBJECTIVE
      3. 9.3 PROCEDURE
      4. 9.4 QUESTIONS
    3. CHAPTER 10: Smith–Waterman Algorithm (Local Alignment)
      1. 10.1 INTRODUCTION
      2. 10.2 OBJECTIVE
      3. 10.3 PROCEDURE
      4. 10.4 QUESTIONS
    4. CHAPTER 11: Sequence Alignment Using Online Tools
      1. 11.1 INTRODUCTION
      2. 11.2 OBJECTIVE
      3. 11.3 PROCEDURE
      4. 11.4 INTERPRETATION OF RESULTS
      5. 11.5 COLOR SCHEME FOR AMINO ACID RESIDUES
      6. 11.6 QUESTIONS
  8. SECTION III: Basic Local Alignment Search Tools
    1. CHAPTER 12: Basic Local Alignment Search Tool for Nucleotide (BLASTn)
      1. 12.1 INTRODUCTION
      2. 12.2 OBJECTIVE
      3. 12.3 PROCEDURE
      4. 12.4 QUESTIONS
    2. CHAPTER 13: Basic Local Alignment Search Tool for Amino Acid Sequences (BLASTp)
      1. 13.1 INTRODUCTION
      2. 13.2 OBJECTIVE
      3. 13.3 PROCEDURE
      4. 13.4 QUESTIONS
    3. CHAPTER 14: BLASTx
      1. 14.1 INTRODUCTION
      2. 14.2 OBJECTIVE
      3. 14.3 PROCEDURE
      4. 14.4 INTERPRETATION OF BLASTx RESULTS
      5. 14.5 QUESTIONS
    4. CHAPTER 15: tBLASTn
      1. 15.1 INTRODUCTION
      2. 15.2 OBJECTIVE
      3. 15.3 PROCEDURE
      4. 15.4 ALGORITHM PARAMETERS
      5. 15.5 INTERPRETATION OF tBLASTn RESULTS
      6. 15.6 QUESTIONS
    5. CHAPTER 16: tBLASTx
      1. 16.1 INTRODUCTION
      2. 16.2 OBJECTIVE
      3. 16.3 PROCEDURE
      4. 16.4 ALGORITHM PARAMETERS
      5. 16.5 INTERPRETATION OF tBLASTx RESULTS
      6. 16.6 QUESTIONS
  9. SECTION IV: Primer Designing and Quality Checking
    1. CHAPTER 17: Primer Designing – Basics
      1. 17.1 INTRODUCTION
      2. 17.2 OTHER IMPORTANT FEATURES FOR DESIGNING “GOOD” PRIMERS
      3. 17.3 QUESTIONS
    2. CHAPTER 18: Designing PCR Primers Using the Primer3 Online Tool
      1. 18.1 INTRODUCTION
      2. 18.2 OBJECTIVE
      3. 18.3 PROCEDURE
      4. 18.4 OUTPUT
      5. 18.5 SELECTION OF THE BEST PRIMER‐PAIRS BY COMPARATIVE EVALUATION OF THE DESIGNED PRIMERS
      6. 18.6 QUESTIONS
    3. CHAPTER 19: Quality Checking of the Designed Primers
      1. 19.1 INTRODUCTION
      2. 19.2 OBJECTIVE
      3. 19.3 PROCEDURE
      4. 19.4 IDT UNAFOLD – CHECKING THE SECONDARY STRUCTURE FORMATION OF THE AMPLICON
      5. 19.5 PRIMER‐BLAST – TO DETECT POSSIBLE SPURIOUS AMPLIFICATION
      6. 19.6 QUESTIONS
    4. CHAPTER 20: Primer Designing for SYBR Green Chemistry of qPCR
      1. 20.1 INTRODUCTION
      2. 20.2 QUESTIONS
  10. SECTION V: Molecular Phylogenetics
    1. CHAPTER 21: Construction of Phylogenetic Tree: Unweighted‐Pair Group Method with Arithmetic Mean (UPGMA)
      1. 21.1 INTRODUCTION
      2. 21.2 ASSUMPTIONS
      3. 21.3 OBJECTIVE
      4. 21.4 PROCEDURE
      5. 21.5 INTERPRETATION OF UPGMA TREE
      6. 21.6 QUESTIONS
    2. CHAPTER 22: Construction of Phylogenetic Tree: Fitch Margoliash (FM) Algorithm
      1. 22.1 INTRODUCTION
      2. 22.2 OBJECTIVE
      3. 22.3 PROCEDURE
      4. 22.4 INTERPRETATION OF THE FM TREE
      5. 22.5 QUESTIONS
    3. CHAPTER 23: Construction of Phylogenetic Tree: Neighbor‐Joining Method
      1. 23.1 INTRODUCTION
      2. 23.2 OBJECTIVE
      3. 23.3 PROCEDURE
      4. 23.4 INTERPRETATION OF NJ TREE
      5. 23.5 QUESTIONS
    4. CHAPTER 24: Construction of Phylogenetic Tree: Maximum Parsimony Method
      1. 24.1 INTRODUCTION
      2. 24.2 OBJECTIVE
      3. 24.3 PROCEDURE
      4. 24.4 INTERPRETATION OF MP TREE
      5. 24.5 QUESTIONS
    5. CHAPTER 25: Construction of Phylogenetic Tree: Minimum Evolution Method
      1. 25.1 INTRODUCTION
      2. 25.2 OBJECTIVE
      3. 25.3 PROCEDURE
      4. 25.4 INTERPRETATION OF THE ME TREE
      5. 25.5 QUESTIONS
    6. CHAPTER 26: Construction of Phylogenetic Tree Using MEGA7
      1. 26.1 INTRODUCTION
      2. 26.2 OBJECTIVE
      3. 26.3 PROCEDURE
      4. 26.4 INTERPRETATION OF PHYLOGENETIC TREE
      5. 26.5 QUESTIONS
    7. CHAPTER 27: Interpretation of Phylogenetic Trees
      1. 27.1 INTRODUCTION
      2. 27.2 UNDERSTANDING PHYLOGENETIC TREES
      3. 27.3 REPRESENTATION OF PHYLOGENETIC TREES
      4. 27.4 METHODS FOR CONSTRUCTING EVOLUTIONARY TREES FROM INFERENCES
      5. 27.5 INFERRING PHYLOGENETIC TREES
      6. 27.6 QUESTIONS
  11. SECTION VI: Protein Structure Prediction
    1. CHAPTER 28: Prediction of Secondary Structure of Protein
      1. 28.1 INTRODUCTION
      2. 28.2 OBJECTIVE
      3. 28.3 SECONDARY STRUCTURE PREDICTION USING ONLINE TOOL PSIPRED
      4. 28.4 SECONDARY STRUCTURE PREDICTION USING THE ONLINE CDM TOOL
      5. 28.5 QUESTIONS
    2. CHAPTER 29: Prediction of Tertiary Structure of Protein: Sequence Homology
      1. 29.1 INTRODUCTION
      2. 29.2 OBJECTIVE
      3. 29.3 PROCEDURE (SWISS‐MODEL PROGRAM)
      4. 29.4 OUTPUT
      5. 29.5 VISUALIZING THE PREDICTED STRUCTURE
      6. 29.6 INTERPRETATION OF RESULTS
      7. 29.7 QUESTIONS
    3. CHAPTER 30: Protein Structure Prediction Using Threading Method
      1. 30.1 INTRODUCTION
      2. 30.2 OBJECTIVE
      3. 30.3 PROCEDURE
      4. 30.4 RESULTS AND INTERPRETATION
      5. 30.5 QUESTIONS
    4. CHAPTER 31: Prediction of Tertiary Structure of Protein: Ab Initio Approach
      1. 31.1 INTRODUCTION
      2. 31.2 OBJECTIVE
      3. 31.3 PROCEDURE (RAPTORX)
      4. 31.4 JOB STATUS
      5. 31.5 OUTPUT AND INTERPRETATION OF RESULTS
      6. 31.6 QUESTIONS
    5. CHAPTER 32: Validation of Predicted Tertiary Structure of Protein
      1. 32.1 INTRODUCTION
      2. 32.2 OBJECTIVE
      3. 32.3 PROCEDURE (WHAT IF TOOL FOR VALIDATING THE 3D STRUCTURE PREDICTION RESULTS)
      4. 32.4 INTERPRETATION OF RESULTS OF WHAT IF
      5. 32.5 MOLPROBITY TOOL FOR RAMACHANDRAN PLOT
      6. 32.6 INTERPRETATION OF RAMACHANDRAN PLOT ANALYSIS
      7. 32.7 QUESTIONS
  12. SECTION VII: Molecular Docking and Binding Site Prediction
    1. CHAPTER 33: Prediction of Transcription Binding Sites
      1. 33.1 INTRODUCTION
      2. 33.2 OBJECTIVE
      3. 33.3 TRANSFAC
      4. 33.4 BINDING SITES SEARCHING USING THE MATCH TOOL
      5. 33.5 QUESTIONS
    2. CHAPTER 34: Prediction of Translation Initiation Sites
      1. 34.1 INTRODUCTION
      2. 34.2 OBJECTIVE
      3. 34.3 PROCEDURE
      4. 34.4 QUESTIONS
    3. CHAPTER 35: Molecular Docking
      1. 35.1 INTRODUCTION
      2. 35.2 OBJECTIVE
      3. 35.3 PROCEDURE
      4. 35.4 RESULT AND INTERPRETATION
      5. 35.5 QUESTIONS
  13. SECTION VIII: Genome Annotation
    1. CHAPTER 36: Genome Annotation in Prokaryotes
      1. 36.1 INTRODUCTION
      2. 36.2 OBJECTIVE
      3. 36.3 PROCEDURE
      4. 36.4 INTERPRETATION OF GENEMARK OUTPUT
      5. 36.5 QUESTIONS
    2. CHAPTER 37: Genome Annotation in Eukaryotes
      1. 37.1 INTRODUCTION
      2. 37.2 OBJECTIVE
      3. 37.3 PROCEDURE
      4. 37.4 INTERPRETATION OF GENSCAN OUTPUT
      5. 37.5 QUESTIONS
  14. SECTION IX: Advanced Biocomputational Analyses
    1. CHAPTER 38: Concepts of Real‐Time PCR Data Analysis
      1. 38.1 INTRODUCTION
      2. 38.2 GETTING STARTED WITH RT‐qPCR
      3. 38.3 PCR FLUORESCENCE CHEMISTRY
      4. 38.4 RT‐qPCR DATA ANALYSIS: GENE EXPRESSION ANALYSIS
      5. 38.5 QUESTIONS
    2. CHAPTER 39: Overview of Microarray Data Analysis
      1. 39.1 CONCEPT
      2. 39.2 GETTING STARTED WITH MICROARRAY
      3. 39.3 MICROARRAY DATA ANALYSIS: GENE EXPRESSION ANALYSIS
      4. 39.4 STEPS INVOLVED IN MICROARRAY DATA ANALYSIS
      5. 39.5 FUNCTIONAL INFORMATION USING GENE NETWORKS AND PATHWAYS
      6. 39.6 LIVESTOCK RESEARCH THAT INVOLVED MICROARRAY ANALYSIS (SOME EXAMPLES)
      7. 39.7 APPLICATIONS OF MICROARRAY
      8. 39.8 QUESTIONS
    3. CHAPTER 40: Single Nucleotide Polymorphism (SNP) Mining Tools
      1. 40.1 INTRODUCTION
      2. 40.2 OBJECTIVE
      3. 40.3 PROCEDURE
      4. 40.4 INTERPRETATION OF RESULTS
      5. 40.5 QUESTIONS
    4. CHAPTER 41: In Silico Mining of Simple Sequence Repeats (SSR) Markers
      1. 41.1 INTRODUCTION
      2. 41.2 OBJECTIVE
      3. 41.3 MISA (MICROSATELLITE IDENTIFICATION TOOL)
      4. 41.4 RESULT
      5. 41.5 QUESTIONS
    5. CHAPTER 42: Basics of RNA‐Seq Data Analysis
      1. 42.1 INTRODUCTION
      2. 42.2 AIM OF AN RNA‐SEQ EXPERIMENT
      3. 42.3 FAST SEQUENCE ALIGNMENT STRATEGIES
      4. 42.4 QUESTIONS
    6. CHAPTER 43: Functional Annotation of Common Differentially Expressed Genes
      1. 43.1 INTRODUCTION
      2. 43.2 FUNCTIONAL ANNOTATION
      3. 43.3 QUESTIONS
    7. CHAPTER 44: Identification of Differentially Expressed Genes (DEGs)
      1. 44.1 SECTION I. QUALITY FILTERING OF DATA USING PRINSEQ
      2. 44.2 SECTION II. IDENTIFICATION OF DIFFERENTIALLY EXPRESSED GENES – I (USING CUFFLINKS)
      3. 44.3 SECTION III. IDENTIFICATION OF DIFFERENTIALLY EXPRESSED GENES – II (USING RSEM‐DE PACKAGES EBSEQ, DESEQ2 AND EDGER)
      4. 44.4 USE OF DE PACKAGES FOR IDENTIFYING THE DIFFERENTIALLY EXPRESSED GENES
      5. 44.5 QUESTIONS
    8. CHAPTER 45: Estimating MicroRNA Expression Using the miRDeep2 Tool
      1. 45.1 INTRODUCTION
      2. 45.2 PREPROCESSING OF READS
      3. 45.3 INPUT FORMATS OF THE DATA FILE
      4. 45.4 OUTPUT FORMATS THAT CAN BE GENERATED
      5. 45.5 PRELIMINARY FILES USED IN THE EXAMPLE
      6. 45.6 QUESTIONS
    9. CHAPTER 46: miRNA Target Prediction
      1. 46.1 INTRODUCTION
      2. 46.2 miRNA TARGET PREDICTION BY TARGETSCAN (http://targetscan.org/)
      3. 46.3 miRNA TARGET PREDICTION BY TARGETSCAN IN HUMAN
      4. 46.4 miRNA TARGET PREDICTION BY psRNATARGET (http://plantgrn.noble.org/psRNATarget>/)
      5. 46.5 miRNA TARGET PREDICTION BY miRANDA (http://www.microrna.org)
      6. 46.6 QUESTIONS
  15. Appendix A: Usage of Internet for Bioinformatics
  16. Appendix B: Important Web Resources for Bioinformatics Databases and Tools
    1. INTRODUCTION
  17. Appendix C: NCBI Database: A Brief Account
  18. Appendix D: EMBL Databases and Tools: An Overview
    1. INTRODUCTION
    2. THE EMBL DATABASES
    3. THE EMBL TOOLS
  19. Appendix E: Basics of Molecular Phylogeny
    1. GEOLOGICAL CLOCK
    2. MORPHOLOGICAL PHYLOGENY TO MOLECULAR PHYLOGENY
    3. BASIS OF MOLECULAR PHYLOGENY
    4. MUTATION RATE
    5. COMPONENTS OF A PHYLOGENETIC TREE
    6. TYPES OF PHYLOGENETIC TREES
  20. Appendix F: Evolutionary Models of Molecular Phylogeny
    1. INTRODUCTION
  21. Glossary
  22. References
  23. Webliography
  24. Index
  25. End User License Agreement