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<p>PREFACE, xi</p> <p>ACKNOWLEDGEMENTS, xiii</p> <p>LIST OF ABBREVIATIONS, xv</p> <p><b>SECTION I Molecular Sequences and Structures</b></p> <p>1 Retrieval of Sequence(s) from the NCBI Nucleotide Database, 3</p> <p>2 Retrieval of Protein Sequence from UniProtKB, 9</p> <p>3 Downloading Protein Structure, 15</p> <p>4 Visualizing Protein Structure, 19</p> <p>5 Sequence Format Conversion, 23</p> <p>6 Nucleotide Sequence Analysis Using Sequence Manipulation Suite (SMS), 31</p> <p>7 Detection of Restriction Enzyme Sites, 43</p> <p><b>SECTION II Sequence Alignment</b></p> <p>8 Dot Plot Analysis, 53</p> <p>9 Needleman–Wunsch Algorithm (Global Alignment), 59</p> <p>10 Smith–Waterman Algorithm (Local Alignment), 67</p> <p>11 Sequence Alignment Using Online Tools, 73</p> <p><b>SECTION III Basic Local Alignment Search Tools</b></p> <p>12 Basic Local Alignment Search Tool for Nucleotide (BLASTn), 81</p> <p>13 Basic Local Alignment Search Tool for Amino Acid Sequences (BLASTp), 91</p> <p>14 BLASTx, 103</p> <p>15 tBLASTn, 109</p> <p>16 tBLASTx, 113</p> <p><b>SECTION IV Primer Designing and Quality Checking</b></p> <p>17 Primer Designing – Basics, 121</p> <p>18 Designing PCR Primers Using the Primer3 Online Tool, 125</p> <p>19 Quality Checking of the Designed Primers, 139</p> <p>20 Primer Designing for SYBR Green Chemistry of qPCR, 147</p> <p><b>SECTION V Molecular Phylogenetics</b></p> <p>21 Construction of Phylogenetic Tree: Unweighted?]Pair Group Method with Arithmetic Mean (UPGMA), 151</p> <p>22 Construction of Phylogenetic Tree: Fitch Margoliash (FM) Algorithm, 159</p> <p>23 Construction of Phylogenetic Tree: Neighbor?]Joining Method, 165</p> <p>24 Construction of Phylogenetic Tree: Maximum Parsimony Method, 175</p> <p>25 Construction of Phylogenetic Tree: Minimum Evolution Method, 183</p> <p>26 Construction of Phylogenetic Tree Using MEGA7, 187</p> <p>27 Interpretation of Phylogenetic Trees, 197</p> <p><b>SECTION VI Protein Structure Prediction</b></p> <p>28 Prediction of Secondary Structure of Protein, 211</p> <p>29 Prediction of Tertiary Structure of Protein: Sequence Homology, 217</p> <p>30 Protein Structure Prediction Using Threading Method, 223</p> <p>31 Prediction of Tertiary Structure of Protein: Ab Initio Approach, 229</p> <p>32 Validation of Predicted Tertiary Structure of Protein, 235</p> <p><b>SECTION VII Molecular Docking and Binding Site Prediction</b></p> <p>33 Prediction of Transcription Binding Sites, 243</p> <p>34 Prediction of Translation Initiation Sites, 251</p> <p>35 Molecular Docking, 257</p> <p><b>SECTION VIII Genome Annotation</b></p> <p>36 Genome Annotation in Prokaryotes, 265</p> <p>37 Genome Annotation in Eukaryotes, 269</p> <p><b>SECTION IX Advanced Biocomputational Analyses</b></p> <p>38 Concepts of Real?]Time PCR Data Analysis, 275</p> <p>39 Overview of Microarray Data Analysis, 283</p> <p>40 Single Nucleotide Polymorphism (SNP) Mining Tools, 289</p> <p>41 In Silico Mining of Simple Sequence Repeats (SSR) Markers, 299</p> <p>42 Basics of RNA?]Seq Data Analysis, 305</p> <p>43 Functional Annotation of Common Differentially Expressed Genes, 313</p> <p>44 Identification of Differentially Expressed Genes (DEGs), 325</p> <p>45 Estimating MicroRNA Expression Using the miRDeep2 Tool, 357</p> <p>46 miRNA Target Prediction, 365</p> <p>Appendices</p> <p>Appendix A: Usage of Internet for Bioinformatics, 377</p> <p>Appendix B: Important Web Resources for Bioinformatics Databases and Tools, 381</p> <p>Appendix C: NCBI Database: A Brief Account, 389</p> <p>Appendix D: EMBL Databases and Tools: An Overview, 395</p> <p>Appendix E: Basics of Molecular Phylogeny, 403</p> <p>Appendix F: Evolutionary Models of Molecular Phylogeny, 411</p> <p>GLOSSARY, 415</p> <p>REFERENCES, 423</p> <p>WEBLIOGRAPHY, 431</p> <p>INDEX, 435</p>

<p><b>About the Authors</b> <p><b>Chandra Sekhar Mukhopadhyay</b> 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. <p><b>Ratan Kumar Choudhary</b> is an Assistant Professor at the School of Animal Biotechnology, Guru Angad Dev Veterinary and Animal Sciences University (GADVASU) at Ludhiana, Punjab, India. <p><b>Mir Asif Iquebal</b> 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.

<p><b>An Accessible Guide that Introduces Students in All Areas of Life Sciences to Bioinformatics</b> <p><i>Basic Applied Bioinformatics</i> 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. <i>Basic Applied Bioinformatics</i> is written as an accessible guide for graduate students studying bioinformatics, biotechnology, and other related sub-disciplines of the life sciences. <p>This 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 updated information on bioinformatics. <p>Salient features of this book include: <ul> <li>Accessible and updated information on bioinformatics tools</li> <li>A practical step-by-step approach to molecular-data analyses</li> <li>Information pertinent to study a variety of disciplines including biotechnology, zoology, bioinformatics and other related fields</li> <li>Worked examples, glossary terms, problems and solutions.</li> </ul> <p><i>Basic Applied Bioinformatics</i> gives students studying bioinformatics, agricultural biotechnology, animal biotechnology, medical biotechnology, microbial biotechnology, and zoology an updated introduction to the growing field of bioinformatics.

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