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Cover Art
PRINTED BOOKS
Author Soh, Jung.

Title Genome annotation / Jung Soh, Paul M.K. Gordon, Christoph W. Sensen.

Published Boca Raton : Taylor & Francis, [2013]
©2013

Copies

Location Call No. Status
 UniM BioMed  572.330285 SOH    AVAILABLE
Physical description xxi, 232 pages, 16 unnumbered pages of plates : illustrations (some colour) ; 24 cm + 1 CD-ROM.
Series Chapman & Hall/CRC mathematical and computational biology series.
Chapman and Hall/CRC mathematical & computational biology series.
Notes "A CRC title."
Bibliography Includes bibliographical references and index.
Contents Chapter 1 DNA Sequencing Strategies 1 -- 1.1 Evolution of DNA Sequencing Technologies 1 -- 1.2 DNA Sequence Assembly Strategies 2 -- 1.3 Next-Generation Sequencing 5 -- 1.4 Sequencing Bias and Error Rates 6 -- References 7 -- Chapter 2 Coding Sequence Prediction 9 -- 2.1 Introduction 9 -- 2.2 Mapping Messenger RNA (mRNA) 9 -- 2.3 Statistical Models 13 -- 2.4 Cross-Species Methods 19 -- 2.5 Combining Gene Predictions 23 -- 2.6 Splice Variants 24 -- References 27 -- Chapter 3 Between the Genes 31 -- 3.1 Introduction 31 -- 3.2 Transcription Factors 31 -- 3.3 RNA 36 -- 3.4 Pseudogenes 44 -- 3.5 Other Repeats 49 -- References 50 -- Chapter 4 Genome-Associated Data 55 -- 4.1 Introduction 55 -- 4.2 Operons 55 -- 4.3 Metagenomics 56 -- 4.4 Individual Genomes 60 -- References 65 -- Chapter 5 Characterization of Gene Function through Bioinformatics: The Early Days 69 -- 5.1 Overview 69 -- 5.2 Stand-Alone Tools and Tools for the Early Internet 71 -- 5.3 Packages 73 -- 5.4 From Fasta Files to Annotated Genomes 77 -- 5.5 Conclusion 79 -- References 79 -- Chapter 6 Visualization Techniques and Tools for Genomic Data 83 -- 6.1 Introduction 83 -- 6.2 Visualization of Sequencing Data 84 -- 6.3 Visualization of Multiple Sequence Alignments 88 -- 6.4 Visualization of Hierarchical Structures 91 -- 6.5 Visualization of Gene Expression Data 96 -- References 101 -- Chapter 7 Functional Annotation 105 -- 7.1 Introduction 105 -- 7.2 Biophysical and Biochemical Feature Prediction 105 -- 7.3 Protein Domains 108 -- 7.4 Similarity Searches 112 -- 7.5 Pairwise Alignment Methods 116 -- 7.6 Conclusion 119 -- References 119 -- Chapter 8 Automated Annotation Systems 125 -- 8.1 Introduction 125 -- 8.2 Magpie 126 -- 8.3 Generic Model Organism Database 135 -- 8.4 AGeS 137 -- 8.5 Ensembl 139 -- 8.6 Summary 142 -- References 143 -- Chapter 9 Dynamic Annotation Systems: End-User-Driven Annotation and Visualization 145 -- 9.1 Introduction 145 -- 9.2 Web-Based Genome Annotation Browsers 146 -- 9.3 Stand-Alone Genome Annotation Browsers 155 -- 9.4 Comparative Visualization of Genomes 162 -- References 169 -- Chapter 10 Web-Based Workflows 173 -- 10.1 Introduction 173 -- 10.2 Principles of Web-Based Workflows 173 -- 10.3 Galaxy 175 -- 10.4 Taverna 179 -- 10.5 Seahawk 183 -- 10.6 Conclusion 192 -- References 192 -- Chapter 11 Analysis Pipelines for Next-Generation Sequencing Data 195 -- 11.1 Introduction 195 -- 11.2 Genome Sequence Reconstruction 196 -- 11.3 Analysis Pipelines: Case Studies 200 -- 11.4 Next-Generation Genome Browsing 205 -- References 210.
Other author Gordon, Paul M. K. (Paul-Michael Kempton), 1976-
Sensen, C. W. (Christoph W.)
Subject Bioinformatics.
Genomics -- Data processing.
Human genome.
ISBN 9781439841174 (hardcover : alk. paper)