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In Silico Genomics and Proteomics: Functional Annotation of Genomes and Proteins
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Editors: Nicola Mulder (EMBL Outstation European Bioinformatics Institute, Hinxston, UK)
Book Description:
The advancement of DNA sequencing technologies has resulted in a movement away from the single gene, and towards a whole genome focus. Previously DNA sequencing was expensive, slow and tedious, but new technologies have been developed that facilitate the relatively cheap and rapid generation of raw sequence from whole bacterial genomes. The sequencing of the human genome was also accelerated in the final phases as a result of new sequencing methods. However, generating the raw sequence is just the start, and tools are required to convert it into useful biological knowledge. This book highlights the new advances in DNA sequencing, and summarizes the process of genome and protein annotation. The book also describes the tools required to achieve this, and provide examples within the context of specific genomes.

Table of Contents:

Part A: Protein Annotation Tools

Chapter 1 - Genomics and the genome era; pp. 3-9
(Nicola Mulder and Rolf Apweiler, still to come)

Chapter 2 - Sequence clustering as a method of protein functional annotation; pp. 11-23
(Robert Petryszak and Paul Kersey)

Chapter 3 - Function prediction with protein signatures and InterPro; pp. 25-36
(Nicola Mulder)

Chapter 4 - The Gene Ontology Annotation (GOA) database, Evelyn Camon, Daniel Barrell; pp. 37-54
(Emily Dimmer and Vivian Lee)

Chapter 5 - Curator driven protein sequence analysis and annotation; pp. 55-70
(Michele Magrane and Claire O’Donovan)

Chapter 6 - Automated annotation of proteins; pp. 71-78
(Ernst Kretschmann and Daniela Wieser)

Chapter 7 - Guilt by association: using protein interactions and expression patterns to predict protein function; pp. 79-88
(Sandra Orchard and Henning Hermjakob)

Part B: Genome Annotation Pipelines and Browsers

Chapter 8 - Artemis and ACT: DNA sequence viewing, annotation and comparison tools; pp. 99-107
(Tim Carver, Stephen Bentley, Nicholas Thomson, Matthew Holden and Julian Parkhill)

Chapter 9 - Ensembl’s annotation pipeline and its use in eukaryotic genomes; pp. 109-123
(Xosé M. Fernández, Steve Searle and Ewan Birney)

Chapter 10 - Genome annotation and viewing in VEGA; pp. 125-146
(Jennifer Harrow and Laurens Wilming)

Chapter 11 - The PEDANT genome database; pp. 147-156
(Dmitrij Frishman, Klaus Heumann and Hans-Werner Mewes)

Chapter 12 - Microbial genomes at NCBI; pp. 157-183
(William Klimke and Tatiana Tatusova)

Chapter 13 - PlasmoDB: the Plasmodium genomics and functional genomics reso0urce; pp. 185-200
(Patricia L. Whetzel, Shailesh V. Date, Kobby Essien, Martin J. Fraunholz, Bindu Gajria, Gregory R. Grant, John Iodice, Jessica C. Kissinger, Philip T. Labo, Arthur J. Milgram, David S. Roos, and Christian J. Stoeckert Jr)

Chapter 14 - Integr8: Navigating Genome Reviews and the Proteome Analysis Database; pp. 201-217
(Paul Kersey, Tamara Kulikova, Manuela Pruess and Rolf Apweiler)


   Binding: Hardcover
   Pub. Date: 2006
   ISBN: 1-59454-995-8
   Status: AV
Status Code Description
AN Announcing
FM Formatting
PP Page Proofs
FP Final Production
EP Editorial Production
PR At Prepress
AP At Press
AV Available
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In Silico Genomics and Proteomics: Functional Annotation of Genomes and Proteins