Basic applied bioinformatics

505 Pages·2017·54.61 MB·English

by  Chandra Sekhar Mukhopadhyay

BASIC APPLIED
BIOINFORMATICS

Basic Applied
Bioinformatics
Chandra Sekhar Mukhopadhyay
Ratan Kumar Choudhary
Mir Asif Iquebal
With contributions from
Ravi GVPPS Kumar, Sarika, Dinesh Kumar, Aditya Prasad
Sahoo, Amit Kumar, Saurabh Jain, Surbhi Panwar,
Ashwani Kumar, Harpreet Kaur Manku
This edition first published 2018
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Library of Congress Cataloging‐in‐Publication Data
Names: Mukhopadhyay, Chandra Sekhar, author. | Choudhary, Ratan Kumar, author. |
Iquebal, Mir Asif, author.
Title: Basic applied bioinformatics / by Chandra Sekhar Mukhopadhyay,
Ratan Kumar Choudhary, Mir Asif Iquebal.
Description: 1st edition. | Hoboken, NJ : Wiley, [2017] | Includes bibliographical
references and index. |
Identifiers: LCCN 2017015387 (print) | LCCN 2017019742 (ebook) |
ISBN 9781119244370 (pdf) | ISBN 9781119244417 (epub) |
ISBN 9781119244332 (hardback)
Subjects: LCSH: Bioinformatics–Textbooks. | BISAC: MEDICAL / Biostatistics.
Classification: LCC QH324.2 (ebook) | LCC QH324.2 .M85 2017 (print) |
DDC 572.80285–dc23
LC record available at https://lccn.loc.gov/2017015387
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Dedicated to students, researchers and professionals

Contents
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
vii
viii ConTenTS
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
ConTenTS ix
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