Computational biology and genome informatics /

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This study contains articles written by experts on a wide range of topics that are associated with the analysis and management of biological information at the molecular level. It contains chapters on RNA and protein structure analysis, DNA computing, sequence mapping, genome comparison, gene expres...

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Detalles Bibliográficos
Clasificación:Libro Electrónico
Otros Autores: Wang, Jason T. L., Wu, Cathy H., Wang, Paul P.
Formato: Electrónico eBook
Idioma:Inglés
Publicado: New Jersey : World Scientific, ©2003.
Temas:
Computational biology.
Genetics > Mathematical models.
Genomics.
Computational Biology > methods
Genomics > methods
Proteomics > methods
Computational Biology
Genomics
Bio-informatique.
Génomique.
NATURE > Reference.
SCIENCE > Life Sciences > General.
SCIENCE > Life Sciences > Biology.
Computational Biology > methods.
Genomics > methods.
Proteomics > methods.
Computational Biology.
Computational biology
Genetics > Mathematical models
Acceso en línea:Texto completo
Tabla de Contenidos:
  • Cover
  • Preface
  • Contents
  • Chapter 1 Exploring RNA Intermediate Conformations with the Massively Parallel Genetic Algorithm
  • 1.1 Introduction
  • 1.2 Algorithmic Implementation
  • Population
  • Basic Algorithm
  • Additional Features
  • 1.3 Data Generation and Analysis
  • Exemplary Biological Systems
  • Population Dynamics and Interactive Visualization
  • Stem Trace and Structurelab
  • Single Run Analysis
  • Multiple Run Analysis
  • Multiple Population Size Analysis
  • 1.4 Biological Application
  • PSTVd
  • hok/sok
  • 1.5 Conclusions
  • Acknowledgment
  • References
  • Authors' Addresses
  • Chapter 2 Introduction to Self-Assembling DNA Nanostructures for Computation and Nanofabrication
  • 2.1 Introduction
  • 2.2 Background
  • Chemistry and Biology of DNA
  • DNA as a Structural Material
  • Design of Base Sequences for DNA Nanoconstruction
  • 2.3 Experiments and Applications
  • DNA-based Computation
  • Algorithmic Self-Assembly
  • Patterned DNA Nanostructures
  • Patterned Immobilization of Other Materials on DNA Arrays
  • 2.4 Summary and Future Directions
  • Possible Future Applications
  • Acknowledgments
  • References
  • Author's Address
  • Chapter 3 Mapping Sequence to Rice FPC
  • 3.1 Introduction
  • 3.2 Overview of FPC
  • 3.3 Mapping Sequence to FPC contigs
  • FSD (FPC Simulated Digest)
  • BSS (BLAST Some Sequence)
  • Merging contigs
  • Anchoring contigs
  • WebFPC
  • 3.4 Discussion
  • Acknowledgments
  • References
  • Authors' Addresses
  • Chapter 4 Graph Theoretic Sequence Clustering Algorithms and Their Applications to Genome Comparison
  • 4.1 Introduction
  • 4.1.1 Database search as a genome annotation tool
  • 4.1.2 Clustering algorithms as a genome annotation tool
  • 4.2 Preliminaries
  • 4.3 Sequence Clustering Algorithms Based on Graph Theory
  • 4.3.1 Matsuda, Ishihara, and Hashimoto algorithm
  • 4.3.2 Matsuda algorithm
  • 4.3.3 COG: cluster of orthologous groups
  • 4.3.4 GeneRAGE
  • 4.4 A New Graph Theoretic Sequence Clustering Algorithm
  • 4.4.1 The basic algorithm
  • 4.4.2 Result from application of the basic algorithm
  • 4.5 BAG: The Extended Clustering Algorithm
  • 4.5.1 Issues with the basic algorithm
  • 4.5.2 Setting the cutoff threshold
  • 4.5.3 The overview of the extended algorithm
  • 4.5.4 AP-TEST
  • 4.5.5 RANGE-TEST
  • 4.5.6 HYPERGRAPH-MERGE
  • 4.5.7 The Algorithm
  • 4.6 Implementation
  • 4.7 Application to Genome Comparison
  • 4.7.1 Splitting families
  • 4.7.2 Merging families
  • 4.8 Conclusion
  • Acknowledgments
  • References
  • Author's Address
  • Chapter 5 The Protein Information Resource for Functional Genomics and Proteomics
  • 5.1 Introduction
  • 5.2 PIR-International Protein Sequence Database
  • Superfamily Classification
  • Evidence Attribution and Bibliography Submission
  • 5.3 PIR Non-Redundant Refence Protein Database
  • 5.4 Integrated Protein Classification Database
  • 5.5 PIR System Distribution
  • PIR Web Access
  • PIR FTP Transfer
  • 5.6 Conclusion
  • Acknowledgments
  • References
  • Author's Address
  • Chapter 6 High-Grade Ore for Data Mining in 3D Structures
  • 6.1 Introduction
  • 6.2 Traditional Quality Measures
  • 6.3 All-Atom Contacts for Assessing Structural Accuracy
  • 6.4.

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