About Book

Bioinformatics has become an important part of many areas of biology. Bioinformatics is an interdisciplinary field that develops methods and software tools for understanding biological data. As an interdisciplinary field of science, bioinformatics combines computer science, statistics, mathematics and engineering to study and process biological data. The goals of bioinformatics are integrative and are aimed at figuring out how combinations of different types of data can be used to understand natural phenomena, including organisms and disease. The development of efficient algorithms for measuring sequence similarity is an important goal of bioinformatics. Another goal of bioinformatics is the extension of experimental data by predictions. Bioinformatics is also used to predict interactions between proteins, given individual structures of the partners. This book on bioinformatics, discusses the recent developments that have taken place in these fields. It focuses on allergen bioinformatics, gel-based proteomics, membrane lipid simulations, RNA‐SEQ data analysis, bioinformatics tools, image data processing, bioinformatics workflows and structural bioinformatics. The various sub-fields of bioinformatics along with technological progress that have future implications are glanced at in this book. It brings forth some of the most innovative concepts and elucidates the unexplored aspects of these fields. It includes contribution of experts and scientists which will provide innovative insights to readers. This book will be useful for students, experts and professionals in the fields of molecular biology, genetics and proteomics.

Preface............................................................................................................v

Chapter 1 Bioinformatics Workflows for Genomic Variant Discovery, Interpretation and Prioritization.............................................................1

Abstract ..................................................................................................1

1. Introduction............................................................................................2

2. Detection of genomic variations........................................................4

3. Clinical interpretation of genomic variations................................13

4. Conclusion............................................................................................15

Chapter 2 Bioinformatics Solutions for Image Data Processing......................27

Abstract.................................................................................................27

1. Introduction..........................................................................................28

2. Data formats in biomedical imaging..............................................29

3. Techniques and methods in medical imaging..............................31

4. Imaging processing solutions...........................................................34

5. Conclusion............................................................................................40

Chapter 3 Bioinformatics Tools and Genomic Resources Available in Understanding the Structure and Function of Gossypium.............44

Abstract.................................................................................................44

1. Introduction..........................................................................................45

2. Genome analysis in cotton ...............................................................46

3. Transcriptome analysis in cotton.....................................................50

4. Small RNA analysis in cotton..........................................................54

5. Epigenome analysis in cotton...........................................................56

6. Future direction...................................................................................60

Acknowledgements.............................................................................61

Chapter 4 Bioinformatics: Basics, Development and Future ...........................77

Abstract ................................................................................................77

1. Introduction..........................................................................................78

2. Bioinformatics help in handling and analysis of the genomics

data, genome annotation, and expression profiling....................81

3. Structural bioinformatics: molecular fol-ding, modeling, and

design....................................................................................................85

4. Biological networks and system biology........................................86

5. Databases..............................................................................................87

6. Software, analysis tools, services, and workflow.........................88

7. Text mining..........................................................................................89

8. Education..............................................................................................90

9. Conclusions and future perspectives..............................................91

Acknowledgements.............................................................................93

Chapter 5 Bioinformatics for RNA‐Seq Data Analysis.....................................107

Abstract ..............................................................................................107

1. Introduction........................................................................................107

2. RNA-seq versus microarray for gene expression profiling

analysis................................................................................................109

3. RNA‐seq library preparation and sequencing platforms..........110

4. Algorithms for RNA‐seq data analysis........................................112

5. New RNA sequencing technologies..............................................122

6. Concluding remarks.........................................................................126

Chapter 6 Bioinformatics for Membrane Lipid Simulations: Models,

Computational Methods, and Web Server Tools..........................137

Abstract ..............................................................................................137

1. Introduction........................................................................................138

2. Force fields for lipid simulation....................................................138

3. Tools for membrane simulation setup and analysis..................148

4. Towards realistic bilayer simulations...........................................151

5. Conclusion..........................................................................................152

Acknowledgements...........................................................................152

Chapter 7 Structural Bioinformatics of Proteins: Predicting the Tertiary and Quaternary Structure of Proteins from Sequence..........................161

1. Introduction........................................................................................161

2. Modeling the tertiary structure of proteins.................................163

3. Modeling the quaternary structure of proteins..........................167

4. Errors in models................................................................................177

5. Integrative modeling........................................................................180

6. Conclusions........................................................................................184

Chapter 8 Application of Bioinformatics Tools in Gel-Based Proteomics .192

1. Introduction........................................................................................192

2. Dataset in gel-based proteomics ...................................................194

3. Ontological classification ................................................................196

4. Hierarchical clustering ....................................................................199

5. Systems and network analysis ......................................................202

6. Concluding remarks ........................................................................207

Chapter 9 Data Integration in Bioinformatics: Current Efforts and Challenges ...............................................................................................215

1. Introduction ......................................................................................215

2. Current efforts of data integration in bioinformatics ...............217

3. Challenges ahead .............................................................................225

4. Conclusions........................................................................................229

Chapter 10 Allergen Bioinformatics: Recent Trends and Developments .....238

1. Introduction........................................................................................238

2. Allergen bioinformatics - a need of the hour ............................239

3. Allergen databases ..........................................................................240

4. Insights from structural bioinformatics .......................................247

5. Conclusion .........................................................................................253

Citation......................................................................................................259

Index...........................................................................................................261

About Author

Bruce Stephane obtained his M.Sc. Degree in Biotechnology from Technical University, Aalborg. He is a Biotechnologist with a strong background in Computational Biology and Bioinformatics at Chemnitz. His current research activities include protein-protein interaction prediction, gene expression analysis and protein sequence analysis in the field of bioinformatics. Stephane has authored a number of articles, journal papers, scientific papers and book chapters on proteomics and bioinformatics. He has been an invited speaker at various national and international conferences.