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

"This book provides 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"--