Bioinformatics (eBook)

Front Cover 1
Title Page 4
Copyright Page 5
Editorial Board for Volume 6 6
Table of Contents 8
Contributors 10
Preface 14
SECTION A: PRINCIPLES 16
Chapter 1 Experimental Design and Analysis of Microarrary Data 16
1. INTRODUCTION 16
2. MICROARRAY PLATFORMS 18
3. APPLICATIONS OF MICROARRAYS WITHINMYCOLOGY AND BIOTECHNOLOGY 24
4. EXPERIMENTAL DESIGN OF MICROARRAY EXPERIMENTS 25
5. SCANNING OF MICROARRAYS AND IMAGE PROCESSING 31
6. ANALYSIS OF MICROARRAY DATA 34
7. CONCLUSION 46
REFERENCES 47
Chapter 2 Methods for Protein Homology Modelling 52
1. INTRODUCTION 52
2. HOMOLOGY MODELLING 53
3. PRACTICAL HOMOLOGY MODELLING 63
4. CONSIDERATIONS FOR MODELLING FUNGAL PROTEINS 69
5. CONCLUSION 71
REFERENCES 72
Chapter 3 Phylogenetic Network Construction Approaches 76
1. INTRODUCTION 76
2. PHYLOGENETIC TREE RECONSTRUCTION METHODS 77
3. EXISTING MECHANISMS OF RETICULATE EVOLUTION 84
4. ALGORITHMS AND SOFTWARE FOR DETECTINGRETICULATE EVOLUTION 91
REFERENCES 107
Chapter 4 Issues in Comparative Fungal Genomics 114
1. INTRODUCTION 114
2. OWNERSHIP OF THE GENOMIC DATA 117
3. HOMOLOGY 118
4. COMPARATIVE GENOMICS 120
5. PHYLOGENETICS 121
6. UNIQUE TARGET SITES IN PESTS 122
7. GENE PREDICTION AND GENE FUNCTION 123
8. COMPARATIVE GENOMICS BETWEEN FUNGI AND OTHER ORGANISMS 125
9. FUNGAL COMPARATIVE GENOMICS 126
10. FUNGAL COMPARATIVE GENOMICS - EVOLUTIONARY BIOLOGY 127
11. FUNGAL COMPARATIVE GENOMICS - FUNGAL BIOLOGY 128
12. FUNGAL COMPARATIVE GENOMICS - ESSENTIAL FUNGAL GENES 129
13. FUNGAL COMPARATIVE GENOMICS - SMALL SCALE STUDIES 130
14. CONCLUSION 130
REFERENCES 131
SECTION B: TOOLS 138
Chapter 5 Fungal Genomic Annotation 138
1. INTRODUCTION 138
2. Gene Discovery in the Fungi 142
3. FUNCTIONAL ANNOTATION 146
4. ANNOTATION PIPELINES 149
5. MANUAL CURATION: IT TAKES A VILLAGE 151
6. CONCLUSION 151
REFERENCES 152
Chapter 6 Bioinformatics Packages for Sequence Analysis 158
1. INTRODUCTION 158
2. NATIONAL CENTER FOR BIOTECHNOLOGY INFORMATION (NCBI) 159
3. SEQUENCE ANALYSIS TOOLS 162
4. MOLECULAR DATABASE 172
5. CONCLUSION 173
REFERENCES 173
Chapter 7 A Survey of Computational Methods Used in Microarray Data Interpretation 176
1. INTRODUCTION 176
Chapter 8 Computational Methods in Genome Research 194
2. MICROARRAY FORMALISM 178
3. CLUSTERING 181
4. BEYOND CLUSTERING 188
5. TOOLS FOR MICROARRAY ANALYSIS 189
6. CURRENT STATUS AND FUTURE APPLICATIONS OF MICROARRAY USAGE 190
7. CONCLUSION 192
REFERENCES 192
Chapter 9 Creating Fungal Pathway/Genome Databases Using Pathway Tools 224
Abstract 224
1 Introduction 224
2 Pathway Tools Computational Inferences 225
3 Pathway/Genome Editors 230
4 Analysis and Visualization 230
5 Pathway Tools Ontologies 237
6 Obtaining Pathway Tools and System Requirements 238
7 How to Learn More 239
8 Summary 239
9 Acknowledgments 239
References 239
Chapter 10 Comparative Genomic Analysis of Glycoylation Pathways in Yeast, Plants and Higher Eukaryotes 242
1. INTRODUCTION 242
2. METABOLIC PATHWAY OF N-GLYCAN BIOSYNTHESIS 244
3. DEFECTIVE MUTANTS 256
4. THE DIVERSITY OF N-GLYCAN STRUCTURES 257
5. ENGINEERING THE GLYCOSYLATION PATHWAY 259
6. CONCLUSION 260
REFERENCES 261
SECTION C: APPLICATIONS 264
Chapter 11 LARaLINK 2.0: Data Mining for Clinical Cytogenetics 264
1. INTRODUCTION 264
2. LARaLINK: THE TECHNICAL FRAMEWORK 268
3. CALCULATIONS 269
4. USING LARaLINK: AN OVERVIEW OF THE SPECIFICATION PROCESS 269
5. LARaLINK'S OUTPUT AND DATA RENDERING 275
6. APPLICATION 287
7. CONCLUSION 289
REFERENCES 289
Chapter 12 Sequence-Based Analysis of Fungal Secretomes 292
1. INTRODUCTION 292
2. SEQUENCE-BASED SECRETOME ANALYSES 294
3. DATA SOURCES AND TOOLS 295
4. SCREENING PROTOCOLS FOR SECRETED PROTEINS 299
5. THE YEAST SECRETOME 300
6. OTHER FUNGAL SECRETOMES 305
7. CONCLUSION 307
REFERENCES 307
Chapter 13 Using Web Agents for Data Mining of Fungal Genomes 312
1. INTRODUCTION 312
2. RESULTS 315
3. CONCLUSION 323
REFERENCES 324
Chapter 14 Searching Biological Databases Using Biolinguistic Methods 326
1. INTRODUCTION 326
2. SEQUENCE REPRESENTATION 330
3. SEQUENCE COMPARISON MEASURES 331
4. DNA SEQUENCE RETRIEVAL 334
5. EXTENSION TO PROTEIN SEQUENCE 337
6. PROTEIN CLASSIFICATION 340
8. CONCLUSION 344
REFERENCES 344
Keyword Index 348