Genomes and Databases on the Internet: A Practical Guide to Functions and Applications
Publisher: Horizon Scientific Press
Authors: P. Rangel and J. Giovannetti University of California, Berkley, California, USA
Publication date: November 2001
ISBN-10: 1-898486-31-X (hbk)
ISBN-13: 978-1-898486-31-2 (hbk)
Pages: xii + 223
A concise yet informative book describing in detail the functions and applications of all the genome databases and related bioscience databases available on the internet. This book is an invaluable resource packed with practical information on the use, purpose and future potential of all the major bioscience internet resources. Aimed at all bioscientists, molecular biologists, microbiologists, biotechnologists, genome scientists.
Why do I need this book, I've got the web ?!
All the major bioscience and genome databases are available on the internet but you'll quickly discover that finding them is a trial. Even then you'll probably have a frustrating time discovering how to make full use of the database, download data, perform interactive searches and comparisons, and take maximum advantage of the multiplicity of resources available. Our book is essential to guide you to the relevant resources and to show you how to make full use of the plethora of information available. You really need this book!!!
(See also our companion book: The Internet for Cell and Molecular Biologists)
Chapter List
PART I MOLECULE DATABASES
Chapter 1. Web Basics
• Client / Server Architecture
• Protocols
HTTP
FTP
CGI
• Technologies
Web Standards
The Web Is Stateless
Javascript vs. Java
Chapter 2. Primary Nucleotide Sequence Databases
• International Collaboration
Data Sharing
ASN.1
Features Table
Taxonomy Database
• Display to the Public
File Formats
The GeneBank Flat File
GBFF Header
Locus
Definition
Accession
Version
Source Organism
Reference
GBFF Body
Features
GBFF Footer
• Database Resources
Data Submission
Web Submission:Webin & BankIt
E-mail
Software: Sequin
Sequence Similarity Tools
Secondary Databases
Taxonomy Browsers
Chapter 3. Primary Protein Sequence Databases
• Primary Protein Sequence Databases
PIR-Protein Sequence Database
PSD Data
Finding Sequences of Interest in the PSD
PSD Sequence Analysis Tools
SWISS-PROT
SWISS-PROT Data (and the reason for TrEMBL)
Data Sources
SWISS-PROT/TrEMBL Search and Download
Other Features: HPI, HAMAP
Other Protein Sequence Databases
OWL
Entrez Protein database
Peptide/Protein Sequence Database (PRF/SEQDB)
Chapter 4. Secondary Nucleotide Databases
• Finding DNA and RNA Secondary Databases
• Site Content
• Site Use
• Secondary Database Examples
Chapter 5. Protein Classification Databases
• Common Attributes
Classification Schemes
Manual vs. Automated
Database Integration
Downloading Files
• Individual Descriptions
iPROCLASS
InterPro
MetaFam
COGs
PROSITE
Pfam
Blocks
ProtoMap
PRINTS
CluSTr
eMOTIF
SBASE
TIGRFAMs
DOMO
ProDom
Others
Chapter 6. Molecular Structure Databases
• Primary (Protein) Structure Databases
Protein Data Bank
General Features of the PDB
PDB Data Retrieval and Format
Data Uniformity and Other Improvements
EBI-Macromolecular Structure Database
Other Protein Structure Databases and Table 6.1
• Secondary Protein Structure Databases
Structure Classification Databases
Homologous Families
Hierarchical Classification
Filtered Data Sets
Secondary Structure Databases: DSSP
• Nucleic Acid Structure Databases
Nucleic Acid Structure Types
NDB (& PDB)
RNABase
• IMB Jena Image Library and others
Chapter 7. Gene Function Databases: Enzymes, Interactions, Expression, and Pathways
• Enzyme Databases
Enzyme Nomenclature (on the web) and EC Numbers
ENZYME, LIGAND, and BRENDA
• Interaction Databases
BRITE
DIP
BIND
ProNet
• Gene Expression (Microarrays) Databases
• Pathway Databases
KEGG
WIT
EMP
TRANSFAC System
CSNDB
PART II GENOMIC RESEARCH
Chapter 8. Genomics Centers
• Entrez Genomes
• EBI Genomes
• TIGR Genomes
• NCGR
Chapter 9. Genomes
• Human Genome Databases
HUGO Gene Nomenclature Committee
Online Mendelian Inheritance in Man (OMIM)
Gene Atlas
EnsEMBL
Genome Data Bank
GeneCards
Allgenes.org
UCSC Golden Path
• Vertebrate Genome Databases
General Vertebrate Databases
Online Mendelian Inheritance in Animals (OMIA)
ARKdb
Mouse
Mouse Genome Informatics
Mouse Genome Database (MGD)
Gene Expression Database (GXD)
Rat
Rat Genome Database (RGD) and Ratmap
• Plant Genome Databases
UK CropNet / ARS GDR
TIGR Plant Genomes
Arabidopsis
AGI TAIR
MATDB
AGR Arabidopsis Genome Resource (UK CropNet)
TIGR's AtDB
Banana Genomics
• Insect Genome Databases
Drosophila
Flybase
The Interactive Fly
Flybrain
FlyView
FlyMove
Mosquito
Mosquito Genomics
• Fungus Genome Databases
Yeast
Saccharomyces Genome Database (SGD)
Yeast Proteome Database (YPD)
MIPS Yeast Genome Database (MYGD)
• Invertebrate Genome Databases
C. elegans
WormBase
AceDB
C. elegans AceDB browser at the Sanger Centre
WormPep
Dictyostelium
Dictybase
• Bacterial Genome Databases
General Bacterial Genome Databases
World Data Centre for Microorganisms (WDCM)
Comprehensive Microbial Resource (CMR)
Microbial Genome Database (MGDB)
HOBACGEN: Homologous Bacterial Genes Database
E. coli
EcoGene Web Site: EcoWeb
E. Coli Genome Center (ECGC)
Colibri
• Organelle Databases
Organelles
Mitochondria
Mitochondria and Beyond
• Virus Genome Databases
General Virus Genome Databases
All the Virology on the WWW
International Committee on Taxonomy of Viruses (ICTV)
Plant Viruses Online
VIDA
HIV
HIV Sequence Database
PART III ONLINE ANALYSIS TOOLS
Chapter 10. Genomics Tools
• Database Query
Entrez
SRS
DBGET (and LinkDB)
Query Example: SRS
• AceDB
• Similarity Search
• Multiple Sequence Alignment
• Phylogenetics
• Gene Identification
• Primers
• Microarray Analysis
Chapter 11. Proteomics Tools
• Protein Analysis Tools at ExPASy
ExPASy: Protein Identification and Characterization
Protein Identification and Characterization
DNA(Protein
Similarity Searches
Pattern and Profile Searches
• Post-Translational Modification Prediction
• Primary Structure Analysis
ExPASy: Protein Sequence to Structure
Secondary Structure Prediction
Tertiary Structure
Transmembrane Regions Detection
ExPASy: Protein Sequence Alignment
Sequence Alignment
• Other Protein Analysis Tools
Other Servers with Tools
3-D Protein Structure
3-D Structure Alignment
3-D Structure Annotation
3-D Structure Viewers
PART IV. GENERAL RESOURCES
Chapter 12. Genome and Database Resources
• Portals
• Literature Search
• Suppliers
• Genome Publications
General Genome Publications
Genome Research
Genomics
Nature's Genome Gateway
GenomeBiology.com
Genomics Today
GenomeWeb
Genome Specific Publications
Dendrome
Rice Genome Newsletter
Human Genome News
(EAN: 9781898486312)
