Bioinformatics - 1st Edition - ISBN: 9780444518071, 9780080463704

Bioinformatics, Volume 6

1st Edition

Editors: Dilip K Arora Randy Berka Gautam Singh
eBook ISBN: 9780080463704
Hardcover ISBN: 9780444518071
Imprint: Elsevier Science
Published Date: 15th August 2006
Page Count: 350
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Table of Contents

Editorial Board for Volume 6



Chapter 1: Experimental Design and Analysis of Microarray Data

1. Introduction

2. Microarray Platforms

3. Applications of Microarrays within Mycology and Biotechnology

4. Experimental Design of Microarray Experiments

5. Scanning of Microarrays and Image Processing

6. Analysis of Microarray Data

7. Conclusion

Chapter 2: Methods for Protein Homology Modelling

1. Introduction

2. Homology Modelling

3. Practical Homology Modelling

4. Considerations for Modelling Fungal Proteins

5. Conclusion

Chapter 3: Phylogenetic Network Construction Approaches

1. Introduction

2. Phylogenetic Tree Reconstruction Methods

3. Existing Mechanisms of Reticulate Evolution

4. Algorithms and Software for Detecting Reticulate Evolution

5. Conclusion

Chapter 4: Issues in Comparative Fungal Genomics

1. Introduction

2. Ownership of the Genomic Data

3. Homology

4. Comparative Genomics

5. Phylogenetics

6. Unique Target Sites In Pests

7. Gene Prediction and Gene Function

8. Comparative Genomics Between Fungi and Other Organisms

9. Fungal Comparative Genomics

10. Fungal Comparative Genomics - Evolutionary Biology

11. Fungal Comparative Genomics - Fungal Biology

12. Fungal Comparative Genomics - Essential Fungal Genes

13. Fungal Comparative Genomics - Small Scale Studies

14. Conclusion

Chapter 5: Fungal Genomic Annotation

1. Introduction

2. Gene Discovery in the Fungi

3. Functional Annotation

4. Annotation Pipelines

5. Manual Curation: It Takes a Village

6. Conclusion

Chapter 6: Bioinformatics Packages for Sequence Analysis

1. Introduction

2. National Center for Biotechnology Information (NCBI)

3. Sequence Analysis Tools

4. Molecular Database

5. Conclusion

Chapter 7: A Survey of Computational Methods Used in Microarray Data Interpretation

1. Introduction

2. Microarray Formalism

3. Clustering

4. Beyond Clustering

5. Tools for Microarray Analysis

6. Current Status and Future Applications of Microarray Usage

7. Conclusion

Chapter 8: Computational Methods in Genome Research

1. Introducion

2. Analysis of Nucleotide and Protein Sequences

3. Genome Annotation

4. Comparative Genomics

5. Protein Structure Prediction

6. Functional Annotation & Classification of Proteins

7. Identification of Vaccine Targets

7. Identification of Vaccine Targets

8. Resources

9. Conclusion

Chapter 9: Creating Fungal Pathway/Genome Databases Using Pathway Tools


1 Introduction

2 Pathway Tools Computational Inferences

3 Pathway/Genome Editors

4 Analysis and Visualization

5 Pathway Tools Ontologies

6 Obtaining Pathway Tools and System Requirements

7 How to Learn More

8 Summary

9 Acknowledgments

Chapter 10: Comparative Genomic Analysis of Glycoylation Pathways in Yeast, Plants and Higher eukaryotes

1. Introduction

2. Metabolic Pathway of N-Glycan Biosynthesis

3. Defective Mutants

4. The Diversity of N-Glycan Structures

5. Engineering the Glycosylation Pathway

6. Conclusion

Chapter 11: Genomic Rearrangement and Disease LARaLINK 2.0: Datamining for Clinical Cytogenetics

1. Introduction

2. Laralink: the Technical Framework

3. Calculations

4. Using Laralink: An Overview of the Specification Process

5. Laralink’s Output and Data Rendering

6. Application

7. Conclusion

Chapter 12: Sequence-Based Analysis of Fungal Secretomes

1. Introduction

2. Sequence-Based Secretome Analyses

3. Data Sources and Tools

4. Screening Protocols for Secreted Proteins

5. The Yeast Secretome

6. Other Fungal Secretomes

7. Conclusion

Chapter 13: Using Web Agents for Data Mining of Fungal Genomes

1. Introduction

2. Results

3. Conclusion

Chapter 14: Searching Biological Databases Using Biolinguistic Methods

1. Introduction

2. Sequence Representation

3. Sequence Comparison Measures

4. DNA Sequence Retrieval

5. Extension to Protein Sequence

6. Protein Classification

7. Multiprocessor Bio-Linguistic Search Engine (BSE)

8. Conclusion

Keyword Index























The advances in genomic technologies, such as microarrays and high throughput sequencing, have expanded the realm of possibilities for capturing data and analyzing it using automated computer driven bioinformatics tools. With the completion of the sequencing of genomes of human and several model organisms, a quest for scientific discoveries being fueled by integrative and multidimensional techniques in mathematics and computational sciences. In this volume, leading researchers and experts have provided an overview of significant concepts from biological, mathematical, and computational perspectives. It provides a high level view of fungal genomic data integration and annotation, classification of proteins and identification of vaccine targets, identification of secretome or secreted proteins in fungal genomes, as well as tools for analyzing microarray expression profiles.

Key Features

  • Provides a survey of theoretical underpinnings on the technological tools and applications
  • Discusses the tools utilized for the annotation of fungal genomes and addresses issues related to automated annotation generation in a high throughput biotechnology environment
  • Describes the applications of the concepts and methodologies presented throughout the book


Physical and computational scientists, life scientists, and all those with mathematical, and computer backgrounds


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© Elsevier Science 2006
Elsevier Science
eBook ISBN:
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Ratings and Reviews

About the Editors

Dilip K Arora Editor

Affiliations and Expertise

Department of Botany, Banaras Hindu University, Varanasi, India

Randy Berka Editor

Affiliations and Expertise

Novozymes Biotech, Inc., Davis, CA, U.S.A.

Gautam Singh Editor

Affiliations and Expertise

Center for Bioinformatics, Department of Computer Science & Engineering, Oakland University, Rochester, MI, U.S.A.