Title Page

Copyright Page

Contents

Preface

Acknowledgements

List of Abbreviations

Section I Molecular Sequences and Structures

Chapter 1 Retrieval of Sequence(s) from the NCBI Nucleotide Database

1.1 Introduction

1.2 Components of the NCBI nucleotide database

1.3 Objectives

1.4 Procedure

1.5 Some useful nucleotide sequence databases of NCBI

1.6 Questions

Chapter 2 Retrieval of Protein Sequence from UniProtKB

2.1 Introduction

2.2 Objective

2.3 Procedure

2.4 Questions

Chapter 3 Downloading Protein Structure

3.1 Introduction

3.2 Objective

3.3 Procedure

3.4 Questions

Chapter 4 Visualizing Protein Structure

4.1 Introduction

4.2 Objective

4.3 Procedure

4.4 Questions

Chapter 5 Sequence Format Conversion

5.1 Introduction

5.2 Objective

5.3 Procedure

5.4 Questions

5.5 Brief description of some of the important molecular sequence formats

Chapter 6 Nucleotide Sequence Analysis Using Sequence Manipulation Suite (SMS)

6.1 Introduction

6.2 Objective

6.3 Procedure

6.4 Format conversion

6.5 Sequence analysis

6.6 Sequence figures

6.7 Random sequences

6.8 Miscellaneous

6.9 Questions

Chapter 7 Detection of Restriction Enzyme Sites

7.1 Introduction

7.2 Objective

7.3 Procedure (using NEBCutter)

7.4 Questions

Section II Sequence Alignment

Chapter 8 Dot Plot Analysis

8.1 Introduction

8.2 Objective

8.3 Procedure

8.4 Parameters of dot plot analysis

8.5 Interpretation

8.6 Questions

Chapter 9 Needleman–Wunsch Algorithm (Global Alignment)

9.1 Introduction

9.2 Objective

9.3 Procedure

9.4 Questions

Chapter 10 Smith–Waterman Algorithm (Local Alignment)

10.1 Introduction

10.2 Objective

10.3 Procedure

10.4 Questions

Chapter 11 Sequence Alignment Using Online Tools

11.1 Introduction

11.2 Objective

11.3 Procedure

11.4 Interpretation of results

11.5 Color scheme for amino acid residues

11.6 Questions

Section III Basic Local Alignment Search Tools

Chapter 12 Basic Local Alignment Search Tool for Nucleotide (BLASTn)

12.1 Introduction

12.2 Objective

12.3 Procedure

12.4 Questions

Chapter 13 Basic Local Alignment Search Tool for Amino Acid Sequences (BLASTp)

13.1 Introduction

13.2 Objective

13.3 Procedure

13.4 Questions

Chapter 14 BLASTx

14.1 Introduction

14.2 Objective

14.3 Procedure

14.4 Interpretation of BLASTx results

14.5 Questions

Chapter 15 tBLASTn

15.1 Introduction

15.2 Objective

15.3 Procedure

15.4 Algorithm parameters

15.5 Interpretation of tBLASTn results

15.6 Questions

Chapter 16 tBLASTx

16.1 Introduction

16.2 Objective

16.3 Procedure

16.4 Algorithm parameters

16.5 Interpretation of tBLASTx results

16.6 Questions

Section IV Primer Designing and Quality Checking

Chapter 17 Primer Designing – Basics

17.1 Introduction

17.2 Other important features for designing “good” primers

17.3 Questions

Chapter 18 Designing PCR Primers Using the Primer3 Online Tool

18.1 Introduction

18.2 Objective

18.3 Procedure

18.4 Output

18.5 Selection of the best primer‐pairs by comparative evaluation of the designed primers

18.6 Questions

Chapter 19 Quality Checking of the Designed Primers

19.1 Introduction

19.2 Objective

19.3 Procedure

19.4 IDT UNAFold – Checking the secondary structure formation of THE amplicon

19.5 Primer-BLAST – to detect possible spurious amplification

19.6 Questions

Chapter 20 Primer Designing for SYBR Green Chemistry of qPCR

20.1 Introduction

20.2 Questions

Section V Molecular Phylogenetics

Chapter 21 Construction of Phylogenetic Tree: Unweighted-Pair Group Method with Arithmetic Mean (UPGMA)

21.1 Introduction

21.2 Assumptions

21.3 Objective

21.4 Procedure

21.5 Interpretation of UPGMA tree

21.6 Questions

Chapter 22 Construction of Phylogenetic Tree: Fitch Margoliash (FM) Algorithm

22.1 Introduction

22.2 Objective

22.3 Procedure

22.4 Interpretation of THE FM Tree

22.5 Questions

Chapter 23 Construction of Phylogenetic Tree: Neighbor-Joining Method

23.1 Introduction

23.2 Objective

23.3 Procedure

23.4 Interpretation of NJ Tree

23.5 Questions

Chapter 24 Construction of Phylogenetic Tree: Maximum Parsimony Method

24.1 Introduction

24.2 Objective

24.3 Procedure

24.4 Interpretation of MP tree

24.5 Questions

Chapter 25 Construction of Phylogenetic Tree: Minimum Evolution Method

25.1 Introduction

25.2 Objective

25.3 Procedure

25.4 Interpretation of THE ME tree

25.5 Questions

Chapter 26 Construction of Phylogenetic Tree Using MEGA7

26.1 Introduction

26.2 Objective

26.3 Procedure

26.4 Interpretation of phylogenetic tree

26.5 Questions

Chapter 27 Interpretation of Phylogenetic Trees

27.1 Introduction

27.2 Understanding phylogenetic trees

27.3 Representation of phylogenetic trees

27.4 Methods for constructing evolutionary trees from inferences

27.5 Inferring phylogenetic trees

27.6 Questions

Section VI Protein Structure Prediction

Chapter 28 Prediction of Secondary Structure of Protein

28.1 Introduction

28.2 Objective

28.3 Secondary structure prediction using online tool PSIPRED

28.4 Secondary structure prediction using the online CDM tool

28.5 Questions

Chapter 29 Prediction of Tertiary Structure of Protein: Sequence Homology

29.1 Introduction

29.2 Objective

29.3 Procedure (SWISS-MODEL program)

29.4 Output

29.5 Visualizing the predicted structure

29.6 Interpretation of results

29.7 Questions

Chapter 30 Protein Structure Prediction Using Threading Method

30.1 Introduction

30.2 Objective

30.3 Procedure

30.4 Results and interpretation

30.5 Questions

Chapter 31 Prediction of Tertiary Structure of Protein: Ab Initio Approach

31.1 Introduction

31.2 Objective

31.3 Procedure (RaptorX)

31.4 Job status

31.5 Output and interpretation of results

31.6 Questions

Chapter 32 Section VI Validation of Predicted Tertiary Structure of Protein

32.1 Introduction

32.2 Objective

32.3 Procedure (WHAT IF tool for validating the 3D structure prediction results)

32.4 Interpretation of results of WHAT IF

32.5 MOLprobity tool for Ramachandran plot

32.6 Interpretation of Ramachandran plot analysis

32.7 Questions

Section VII Molecular Docking and Binding Site Prediction

Chapter 33 Prediction of Transcription Binding Sites

33.1 Introduction

33.2 Objective

33.3 TRANSFAC

33.4 Binding sites searching using the MATCH tool

33.5 Questions

Chapter 34 Prediction of Translation Initiation Sites

34.1 Introduction

34.2 Objective

34.3 Procedure

34.4 Questions

Chapter 35 Molecular Docking

35.1 Introduction

35.2 Objective

35.3 Procedure

35.4 Result and interpretation

35.5 Questions

Section VIII Genome Annotation

Chapter 36 Genome Annotation in Prokaryotes

36.1 Introduction

36.2 Objective

36.3 Procedure

36.4 Interpretation of GeneMark output

36.5 Questions

Chapter 37 Genome Annotation in Eukaryotes

37.1 Introduction

37.2 Objective

37.3 Procedure

37.4 Interpretation of GENSCAN output

37.5 Questions

Section IX Advanced Biocomputational Analyses

Chapter 38 Concepts of Real-Time PCR Data Analysis

38.1 Introduction

38.2 Getting started with RT-qPCR

38.3 PCR fluorescence chemistry

38.4 RT-qPCR data analysis: gene expression analysis

38.5 Questions

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

40.1 Introduction

40.2 Objective

40.3 Procedure

40.4 Interpretation of results

40.5 Questions

Chapter 41 In Silico Mining of Simple Sequence Repeats (SSR) Markers

41.1 Introduction

41.2 Objective

41.3 MISA (MIcroSAtellite Identification Tool)

41.4 Result

41.5 Questions

Chapter 42 Basics of RNA-Seq Data Analysis

42.1 Introduction

42.2 Aim of an RNA‐seq experiment

42.3 Fast sequence alignment strategies

42.4 Questions

Chapter 43 Functional Annotation of Common Differentially Expressed Genes

43.1 Introduction

43.2 Functional annotation

43.3 Questions

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

45.1 Introduction

45.2 Preprocessing of reads

45.3 Input formats of the data file

45.4 Output formats that can be generated

45.5 Preliminary files used in the example

45.6 Questions

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

Introduction

Appendix C: NCBI Database: A Brief Account

Appendix D: EMBL Databases and Tools: An Overview

Introduction

The EMBL Databases

The EMBL Tools

Appendix E: Basics of Molecular Phylogeny

Geological Clock

Morphological Phylogeny to Molecular Phylogeny

Basis of Molecular Phylogeny

Mutation Rate

Components of a Phylogenetic Tree

Types of Phylogenetic Trees

Appendix F: Evolutionary Models of Molecular Phylogeny

Introduction

Glossary

References

Webliography

Index

Supplemental Images

EULA