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• Cover image
• Title page
• Table of Contents
• Front Matter
• Applied Mycology and Biotechnology
• Copyright page
• 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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