Bioinformatics and Functional Genomics

Table 1-1. Three primary bioinformatics web servers that serve as centralized repositories for DNA and protein sequence data. These will be introduced in Chapter 2.

Resource	Description
DNA Data Bank of Japan (DDBJ)	Associated with the Center for Information Biology
European Bioinformatics Institute (EBI)	Maintains the EMBL database
National Center for Biotechnology Information (NCBI)	Maintains GenBank

 

Table 1-2. Additional bioinformatics web servers. Each of these web sites contains access to dozens of software tools, research projects, literature references, and other information relevant to bioinformatics.

Resource	Description
ExPASy (Expert Protein Analysis System)	Proteomics server of the Swiss Institute of Bioinformatics
GENESTREAM	Institut de Génétique Humaine, Montpellier
GenomeNet	In Kyoto
INFOBIOGEN	In Montpellier
Oak Ridge National Laboratory (ORNL)	In Tennessee
Protein Information Resource (PIR)	A Division of National Biomedical Research Foundation
The Wellcome Trust Sanger Institute	A genome research center in Cambridge
The Institute for Genomic Research (TIGR)	In Rockville, Maryland

 

Table 1-3. In addition to the bioinformatics servers listed in Tables 1-1 and 1-2, there are many other sites that collect information and resources that are generally useful.

Resource	Description
Amos' WWW links page	From ExPASy
DBCAT, The Public Catalog of Databases	From INFOBIOGEN
European Molecular Biology Network	Various European nodes
Centre for Molecular and Biomolecular Informatics	From the University of Nijmegen

 

Table 1-4. Collections of bioinformatics tools on the web.

Resource	Description
Biology WorkBench	From the University of California at San Diego
Genetics Computer Group (GCG)	Also called the Wisconsin package
Sequence Analysis Software	From Stanford University