Bioinformatics

Editorial Board for Volume 6

Contributors

Preface

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

Abstract

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

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M

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V

W