Basic applied bioinformatics / Chandra Sekhar Mukhopadhyay, Ratan Kumar Choudhary, Mir Asif Iquebal ; with contributions from Ravi GVPPS Kumar [and 8 others].

Format:

Book

Author/Creator:

Mukhopadhyay, Chandra Sekhar, author.

Choudhary, Ratan Kumar, author.

Iquebal, Mir Asif, author.

Contributor:

ProQuest ebook central.

Language:

English

Subjects (All):

Bioinformatics--Textbooks.

Bioinformatics.

Genre:

Textbooks.

Physical Description:

1 online resource

Place of Publication:

Hoboken, NJ : John Wiley & Sons, Inc., 2018.

System Details:

text file

Summary:

Basic Applied Bioinformatics provides practical guidance in bioinformatics and helps students to optimize parameters for data analysis and then to draw accurate conclusion from the result. In addition to parameters optimization, the text will also familiarize students with relevant terminology. Basic Applied Bioinformatics is written as an accessible guide for graduate students studying bioinformatics, biotechnology, and other related sub-disciplines of the life sciences. 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 author, 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. Salient features of this book include: Accessible and updated information on bioinformatics tools, A practical step-by-step approach to molecular-data analyses, Information pertinent to study a variety of disciplines including biotechnology Zoology, bioinformatics and other related field, Worked examples, glossary terms, problems and solutions. Basic Appendix Bioinformatics gives students studying bioinformatics, agricultural biotechnology, animal biotechnology, medical biotechnology, and Zoology an updated introduction to the growing field of bioinformatics. Book jacket.

Contents:

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.

Notes:

Includes bibliographical references and index.

Electronic reproduction. Ann Arbor, MI Available via World Wide Web.

Description based on online resource; title from digital title page (viewed on November 02, 2017).

Other Format:

Print version: Mukhopadhyay, Chandra Sekhar, author. Basic applied bioinformatics

ISBN:

9781119244417

1119244412

9781119244370

1119244374

Publisher Number:

99974067507

Access Restriction:

Restricted for use by site license.