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Basic Applied Bioinformatics

A Beginners′ Guide for Students

Specificaties
Gebonden, 472 blz. | Engels
John Wiley & Sons | e druk, 2017
ISBN13: 9781119244332
Rubricering
John Wiley & Sons e druk, 2017 9781119244332
Verwachte levertijd ongeveer 9 werkdagen

Samenvatting

An accessible guide that introduces students in all areas of life sciences to bioinformatics

Basic Applied Bioinformatics provides a 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. 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 accessible 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 an updated information on bioinformatics.

Salient features of this book includes:

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 fields
Worked examples, glossary terms, problems and solutions

Basic Applied Bioinformatics gives students studying bioinformatics, agricultural biotechnology, animal biotechnology, medical biotechnology, microbial biotechnology, and zoology an updated introduction to the growing field of bioinformatics.

Specificaties

ISBN13:9781119244332
Taal:Engels
Bindwijze:gebonden
Aantal pagina's:472

Inhoudsopgave

<p>Dedication</p>
<p>Preface</p>
<p>Acknowledgements</p>
<p>List Of Abbreviations</p>
<p>i. Molecular Sequences and Structures Page</p>
<p>1 Retrieval of Sequence(s) from NCBI Nucleotide Database<br />CS Mukhopadhyay; RK Choudhary</p>
<p>2 Retrieval of Protein Sequence from UniProtKB<br />CS Mukhopadhyay; RK Choudhary</p>
<p>3 Downloading Protein Structure<br />CS Mukhopadhyay; RK Choudhary</p>
<p>4 Visualizing Protein Structure<br />CS Mukhopadhyay; RK Choudhary</p>
<p>5 Sequence Format Conversion<br />CS Mukhopadhyay; RK Choudhary</p>
<p>6 Nucleotide Sequence Analysis using Sequence Manipulation Suite (SMS)<br />CS Mukhopadhyay; RK Choudhary</p>
<p>7 Detection of&nbsp; Restriction Enzyme Sites<br />CS Mukhopadhyay; RK Choudhary</p>
<p>ii. Sequence Alignment</p>
<p>8 Dot Plot Analysis<br />CS Mukhopadhyay; RK Choudhary</p>
<p>9 Needleman–Wunsch Algorithm (Global Alignment)<br />CS Mukhopadhyay; RK Choudhary</p>
<p>10 Smith–Waterman Algorithm (Local Alignment)<br />CS Mukhopadhyay; RK Choudhary</p>
<p>11 Sequence Alignment using Online Tools<br />CS Mukhopadhyay; RK Choudhary</p>
<p>iii. Basic Local Alignment Search Tools</p>
<p>12 Basic Local Alignment Search Tool for nucleotide (BLASTn)<br />CS Mukhopadhyay; RK Choudhary</p>
<p>13 Basic Local Alignment Search Tool for Amino Acid Sequences (BLASTp)<br />CS Mukhopadhyay; RK Choudhary</p>
<p>14 BLASTx<br />CS Mukhopadhyay; RK Choudhary</p>
<p>15 tBLASTn<br />CS Mukhopadhyay; RK Choudhary</p>
<p>16 tBLASTx<br />CS Mukhopadhyay; RK Choudhary</p>
<p>iv. Primer Designing and Quality Checking</p>
<p>17 Primer Designing– Basics<br />CS Mukhopadhyay; RK Choudhary</p>
<p>18 Designing of PCR Primers using Primer3 Online Tool<br />CS Mukhopadhyay; RK Choudhary</p>
<p>19 Quality Checking of the Designed Primers<br />CS Mukhopadhyay; RK Choudhary</p>
<p>20 Primer Designing for SYBR Green Chemistry of qPCR<br />CS Mukhopadhyay; RK Choudhary</p>
<p>v. Molecular Phylogenetics</p>
<p>21 Construction of Phylogenetic Tree: Unweighted Pair Group Method with Arithmetic mean (UPGMA)<br />CS Mukhopadhyay; RK Choudhary</p>
<p>22 Construction of Phylogenetic tree: Fitch Margoliash (FM) Algorithm<br />CS Mukhopadhyay; RK Choudhary</p>
<p>23 Construction of Phylogenetic tree: Neighbor Joining Method<br />CS Mukhopadhyay; RK Choudhary</p>
<p>24 Construction of Phylogenetic Tree: Maximum Parsimony Method<br />CS Mukhopadhyay; RK Choudhary</p>
<p>25 Construction of Phylogenetic tree: Minimum Evolution Method<br />CS Mukhopadhyay; RK Choudhary</p>
<p>26 Construction of Phylogenetic Tree using MEGA7<br />CS Mukhopadhyay; RK Choudhary</p>
<p>27 Interpretation of Phylogenetic Trees<br />CS Mukhopadhyay; RK Choudhary</p>
<p>vi. Protein Structure Prediction</p>
<p>28 Prediction of Secondary Structure of Protein<br />CS Mukhopadhyay; RK Choudhary</p>
<p>29 Prediction of Tertiary Structure of Protein: Sequence Homology<br />CS Mukhopadhyay; RK Choudhary</p>
<p>30 Protein Structure Prediction using Threading Method<br />CS Mukhopadhyay; HK Manku</p>
<p>31 Prediction of Tertiary Structure of Protein: Ab Initio Approach<br />CS Mukhopadhyay; RK Choudhary</p>
<p>32 Validation of Predicted Tertiary Structure Protein<br />CS Mukhopadhyay; RK Choudhary</p>
<p>vii. Molecular Docking and Binding Site Prediction</p>
<p>33 Predicting Transcription Binding Sites<br />S Jain; S Panwar; A Kumar</p>
<p>34 Predicting Translation Initiation Sites<br />S Jain; S Panwar; A Kumar</p>
<p>35 Docking of Ligand Receptors<br />CS Mukhopadhyay; HK Manku</p>
<p>viii. Genome Annotation</p>
<p>36 Genome Annotation in Prokaryotes<br />CS Mukhopadhyay; RK Choudhary</p>
<p>37 Genome Annotation in Eukaryotes<br />CS Mukhopadhyay; RK Choudhary</p>
<p>ix. Advanced Biocomputational Analyses</p>
<p>38 Concepts of Real Time PCR Data Analysis<br />RK Choudhary</p>
<p>39 Overview of Micro–array Data Analysis<br />RK Choudhary</p>
<p>40 Single Nucleotide Polymorphism (SNP) Mining Tools<br />MA Iquebal; Sarika; D Kumar</p>
<p>41 In silico Mining of Simple Sequence Repeats (SSR) Markers<br />MA Iquebal; Sarika; D Kumar</p>
<p>42 Basics of RNA–Seq Data Analysis<br />GVPPSR Kumar; AP Sahoo; A Kumar</p>
<p>43 Functional Annotation of Common Differentially Expressed Genes<br />GVPPSR Kumar; AP Sahoo; A Kumar</p>
<p>44 Identification of Differentially Expressed Genes (DEGs)<br />GVPPSR Kumar; A Kumar; AP Sahoo</p>
<p>45 Estimating MicroRNA expression using miRDeep2 tool<br />GVPPSR Kumar; A Kumar; AP Sahoo</p>
<p>46 In silico prediction of miRNA Targets<br />Sarika; MA Iquebal; D Kumar</p>
<p>x. Appendices</p>
<p>App. A Usage of Internet for Bioinformatics<br />RK Choudhary</p>
<p>App. B Important Web–Resources for Bioinformatics Databases and Tools<br />CS Mukhopadhyay; RK Choudhary</p>
<p>App. C Usage of NCBI Database Resources<br />CS Mukhopadhyay; RK Choudhary</p>
<p>App. D Usage of Important EMBL Tools<br />S Jain; S Panwar; A Kumar</p>
<p>App. F Evolutionary Models of Molecular Phylogeny<br />CS Mukhopadhyay; RK Choudhary</p>
<p>&nbsp;</p>

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