Genome Information Broker (GIB)
You can help EcoliWiki by editing the content of this page. For information about becoming a registered user and obtaining editing privileges, see Help:Accounts.
<protect>
| Link/URL: | |
|---|---|
| What: |
Comprehensive database of complete microbial genomes |
| Who: |
DNA Data Bank of Japan |
| Updates: | |
| Upcoming events: | |
| Web Services: |
|
| edit table |
</protect>
Contents
About Genome Information Broker (GIB)
The Genome Information Broker (GIB)[1] is a data resource for many micribial genomes.
Content
The top level page lists the available genomes grouped by taxonomy. Clicking on display level arrows near the top of the page changes the granularity of the display. GIB has information on 377 genomes as of Aug 13, 2006, including eubacteria, archaea, and a few eukaryotic microbes (and Arabidopsis, for some reason).
GIB provides a list of links to "genome projects", which are actually a subset of the online data resources for different genomes. Thus, GIB links to EcoCyc, EcoGene, and the E. coli Genome Project at UW-Madison (but not to ASAP, which has more up-to-date information).
The downloads link at GIB goes to an FTP site where gzipped files are available for information in several different formats.
Using Genome Information Broker (GIB)
Browsing
Clicking on a particular genome in GIB brings up a display in the right frame. The display is a graphical genome browser that allows different kinds of views, either of the whole genome, or of a specified region. There are links to display GC content, and control inputs to jump to a particular region. Within a region, you can get a graphical view with color-coded features, or a list of features, or the DNA sequence. The page also has links for BLAST and FASTA searches against the target genome, and keyword searches. Each page also has a link to a help page.
Searching
The keyword search allows you to enter a textword and search against different features in the data set. Features include coding sequences (cds), different kinds of RNAs, replication origins, or miscellaneous features. Searching gives a list of hits and a button that allows you to view their positions on the genome.
Usage examples
Add links to additional pages describing success stories here.
Technology
GIB uses PostGRES as the relational database engine, and PHP to generate web pages.
Web Services/API
Discussion
References
See Help:References for how to manage references in EcoliWiki.
External Links
Genome Information Broker (GIB) URL: http://gib.genes.nig.ac.jp/
