Basic Applied Bioinformatics

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, xiACKNOWLEDGEMENTS, xiiiLIST OF ABBREVIATIONS, xvSECTION I Molecular Sequences and Structures1 Retrieval of Sequence(s) from the NCBI Nucleotide Database, 32 Retrieval of Protein Sequence from UniProtKB, 93 Downloading Protein Structure, 154 Visualizing Protein Structure, 195 Sequence Format Conversion, 236 Nucleotide Sequence Analysis Using Sequence Manipulation Suite (SMS), 317 Detection of Restriction Enzyme Sites, 43SECTION II Sequence Alignment8 Dot Plot Analysis, 539 Needleman–Wunsch Algorithm (Global Alignment), 5910 Smith–Waterman Algorithm (Local Alignment), 6711 Sequence Alignment Using Online Tools, 73SECTION III Basic Local Alignment Search Tools12 Basic Local Alignment Search Tool for Nucleotide (BLASTn), 8113 Basic Local Alignment Search Tool for Amino Acid Sequences (BLASTp), 9114 BLASTx, 10315 tBLASTn, 10916 tBLASTx, 113SECTION IV Primer Designing and Quality Checking17 Primer Designing – Basics, 12118 Designing PCR Primers Using the Primer3 Online Tool, 12519 Quality Checking of the Designed Primers, 13920 Primer Designing for SYBR Green Chemistry of qPCR, 147SECTION V Molecular Phylogenetics21 Construction of Phylogenetic Tree: Unweighted]Pair Group Method with Arithmetic Mean (UPGMA), 15122 Construction of Phylogenetic Tree: Fitch Margoliash (FM) Algorithm, 15923 Construction of Phylogenetic Tree: Neighbor]Joining Method, 16524 Construction of Phylogenetic Tree: Maximum Parsimony Method, 17525 Construction of Phylogenetic Tree: Minimum Evolution Method, 18326 Construction of Phylogenetic Tree Using MEGA7, 18727 Interpretation of Phylogenetic Trees, 197SECTION VI Protein Structure Prediction28 Prediction of Secondary Structure of Protein, 21129 Prediction of Tertiary Structure of Protein: Sequence Homology, 21730 Protein Structure Prediction Using Threading Method, 22331 Prediction of Tertiary Structure of Protein: Ab Initio Approach, 22932 Validation of Predicted Tertiary Structure of Protein, 235SECTION VII Molecular Docking and Binding Site Prediction33 Prediction of Transcription Binding Sites, 24334 Prediction of Translation Initiation Sites, 25135 Molecular Docking, 257SECTION VIII Genome Annotation36 Genome Annotation in Prokaryotes, 26537 Genome Annotation in Eukaryotes, 269SECTION IX Advanced Biocomputational Analyses38 Concepts of Real]Time PCR Data Analysis, 27539 Overview of Microarray Data Analysis, 28340 Single Nucleotide Polymorphism (SNP) Mining Tools, 28941 In Silico Mining of Simple Sequence Repeats (SSR) Markers, 29942 Basics of RNA]Seq Data Analysis, 30543 Functional Annotation of Common Differentially Expressed Genes, 31344 Identification of Differentially Expressed Genes (DEGs), 32545 Estimating MicroRNA Expression Using the miRDeep2 Tool, 35746 miRNA Target Prediction, 365AppendicesAppendix A: Usage of Internet for Bioinformatics, 377Appendix B: Important Web Resources for Bioinformatics Databases and Tools, 381Appendix C: NCBI Database: A Brief Account, 389Appendix D: EMBL Databases and Tools: An Overview, 395Appendix E: Basics of Molecular Phylogeny, 403Appendix F: Evolutionary Models of Molecular Phylogeny, 411GLOSSARY, 415REFERENCES, 423WEBLIOGRAPHY, 431INDEX, 435