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Bioinformatics
- 1st Edition, Volume 6 - August 15, 2006
- Editors: Dilip K Arora, Randy Berka, Gautam B. Singh
- Language: English
- Hardback ISBN:9 7 8 - 0 - 4 4 4 - 5 1 8 0 7 - 1
- Paperback ISBN:9 7 8 - 0 - 4 4 4 - 5 5 0 4 2 - 2
- eBook ISBN:9 7 8 - 0 - 0 8 - 0 4 6 3 7 0 - 4
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… Read more
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Request a sales quoteThe advances in genomic technologies, such as microarrays and high throughput sequencing,have expanded the realm of possibilities for capturing data and analyzing it using automatedcomputer driven bioinformatics tools. With the completion of the sequencing of genomes ofhuman and several model organisms, a quest for scientific discoveries being fueled byintegrative and multidimensional techniques in mathematics and computational sciences. Inthis volume, leading researchers and experts have provided an overview of significantconcepts 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 expressionprofiles.
- 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
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
A
B
C
D
E
F
G
H
I
K
L
M
N
O
P
R
S
T
U
V
W
- No. of pages: 350
- Language: English
- Edition: 1
- Volume: 6
- Published: August 15, 2006
- Imprint: Elsevier Science
- Hardback ISBN: 9780444518071
- Paperback ISBN: 9780444550422
- eBook ISBN: 9780080463704
DA
Dilip K Arora
Affiliations and expertise
Department of Botany, Banaras Hindu University, Varanasi, IndiaRB
Randy Berka
Affiliations and expertise
Novozymes Biotech, Inc., Davis, CA, U.S.A.GS
Gautam B. Singh
Affiliations and expertise
Center for Bioinformatics, Department of Computer Science & Engineering, Oakland University, Rochester, MI, U.S.A.Read Bioinformatics on ScienceDirect