Basic Applied Bioinformatics (eBook)

About the Authors Chandra Sekhar Mukhopadhyay is an Assistant Scientist (Senior Scale) at the School of Animal Biotechnology, Guru Angad Dev Veterinary and Animal Sciences University (GADVASU) at Ludhiana, Punjab, India. Ratan Kumar Choudhary is an Assistant Professor at the School of Animal Biotechnology, Guru Angad Dev Veterinary and Animal Sciences University (GADVASU) at Ludhiana, Punjab, India. Mir Asif Iquebal is a Scientist at the Centre for Agricultural Bioinformatics, Indian Council of Agricultural Research-Indian Agricultural Statistics and Research Institute (ICAR-IASRI) at Pusa, New Delhi, India.

PREFACE, xi

ACKNOWLEDGEMENTS, xiii

LIST OF ABBREVIATIONS, xv

SECTION I Molecular Sequences and Structures

1 Retrieval of Sequence(s) from the NCBI Nucleotide Database, 3

2 Retrieval of Protein Sequence from UniProtKB, 9

3 Downloading Protein Structure, 15

4 Visualizing Protein Structure, 19

5 Sequence Format Conversion, 23

6 Nucleotide Sequence Analysis Using Sequence Manipulation Suite (SMS), 31

7 Detection of Restriction Enzyme Sites, 43

SECTION II Sequence Alignment

8 Dot Plot Analysis, 53

9 Needleman-Wunsch Algorithm (Global Alignment), 59

10 Smith-Waterman Algorithm (Local Alignment), 67

11 Sequence Alignment Using Online Tools, 73

SECTION III Basic Local Alignment Search Tools

12 Basic Local Alignment Search Tool for Nucleotide (BLASTn), 81

13 Basic Local Alignment Search Tool for Amino Acid Sequences (BLASTp), 91

14 BLASTx, 103

15 tBLASTn, 109

16 tBLASTx, 113

SECTION IV Primer Designing and Quality Checking

17 Primer Designing - Basics, 121

18 Designing PCR Primers Using the Primer3 Online Tool, 125

19 Quality Checking of the Designed Primers, 139

20 Primer Designing for SYBR Green Chemistry of qPCR, 147

SECTION V Molecular Phylogenetics

21 Construction of Phylogenetic Tree: Unweighted?]Pair Group Method with Arithmetic Mean (UPGMA), 151

22 Construction of Phylogenetic Tree: Fitch Margoliash (FM) Algorithm, 159

23 Construction of Phylogenetic Tree: Neighbor?]Joining Method, 165

24 Construction of Phylogenetic Tree: Maximum Parsimony Method, 175

25 Construction of Phylogenetic Tree: Minimum Evolution Method, 183

26 Construction of Phylogenetic Tree Using MEGA7, 187

27 Interpretation of Phylogenetic Trees, 197

SECTION VI Protein Structure Prediction

28 Prediction of Secondary Structure of Protein, 211

29 Prediction of Tertiary Structure of Protein: Sequence Homology, 217

30 Protein Structure Prediction Using Threading Method, 223

31 Prediction of Tertiary Structure of Protein: Ab Initio Approach, 229

32 Validation of Predicted Tertiary Structure of Protein, 235

SECTION VII Molecular Docking and Binding Site Prediction

33 Prediction of Transcription Binding Sites, 243

34 Prediction of Translation Initiation Sites, 251

35 Molecular Docking, 257

SECTION VIII Genome Annotation

36 Genome Annotation in Prokaryotes, 265

37 Genome Annotation in Eukaryotes, 269

SECTION IX Advanced Biocomputational Analyses

38 Concepts of Real?]Time PCR Data Analysis, 275

39 Overview of Microarray Data Analysis, 283

40 Single Nucleotide Polymorphism (SNP) Mining Tools, 289

41 In Silico Mining of Simple Sequence Repeats (SSR) Markers, 299

42 Basics of RNA?]Seq Data Analysis, 305

43 Functional Annotation of Common Differentially Expressed Genes, 313

44 Identification of Differentially Expressed Genes (DEGs), 325

45 Estimating MicroRNA Expression Using the miRDeep2 Tool, 357

46 miRNA Target Prediction, 365

Appendices

Appendix A: Usage of Internet for Bioinformatics, 377

Appendix B: Important Web Resources for Bioinformatics Databases and Tools, 381

Appendix C: NCBI Database: A Brief Account, 389

Appendix D: EMBL Databases and Tools: An Overview, 395

Appendix E: Basics of Molecular Phylogeny, 403

Appendix F: Evolutionary Models of Molecular Phylogeny, 411

GLOSSARY, 415

REFERENCES, 423

WEBLIOGRAPHY, 431

INDEX, 435