pgd: home [db=pgd]
Welcome to the e. coli Plasmid Genome Database System

This website is built on top of a Chado comparative database and provides a number of tools for analyzing and visualizing the data.

The PGD relies on pre-computed searches -- primarily BLASTP searches and protein clustering analyses -- the results of which are stored in the comparative database and queried as needed.

  Here is a summary of where you can go from this page and how to move around this particular PGD:
  • Click on the thumbnails below to generate visualizations of the data. From these visualizations you can drill down further by clicking on the features displayed in the images.
  • To find a specific gene use the "Search for genes/proteins" tool below.
  • You will find a summary of the analyses and organisms loaded at the bottom-right of the page
  • Click on the "help" link at the top-right of any section to get more information.
  • Click on the PDG link in the top-right corner or the left hand sidebar of any page to return to this home page.
  • For help or to report bugs use the e-mail link in the bottom-right corner of every page.

To have added functionality and access to additional data of the PGD you must be an authorized user, please email us at Nolan Lab with your requests

Get Firefox

Note: This site has only been tested fully with the Mozilla Firefox browser. Some features will not work properly in other browsers.

Version/News/Updates

PGD site release v0.70 Beta on 5/12/2009

The PGD is currently in Beta testing and is constantly being updated on the backend with new e. coli plasmid sequences that are related to APEC. Along with our in-house sequenced plasmids that we currently completing. If there are any anomalies with the site please email technical support (bottom right of every page).

[Updates] - Built with the help of Sybil you can view all of the changes/updates to the Sybil code here.

Support
Funding for this project provided by the NSF
Analyses/computes all analyses/computes loaded into chado [help]
program / version date description
RBS / RBS_version 2008-10-22 00:12:00 RBS / RBS_version
genbank2bsml / current 2009-08-05 17:04:00 genbank2bsml pAPEC Cryptic 1
TERM / TERM_version 2008-10-22 00:12:00 TERM / TERM_version
j_ortholog_clusters / 2.0 2008-10-22 13:50:00 Ortholog Clusters
wu-blastp / 2.0 2008-10-22 14:38:00 All vs. All wu-blastp
TERM / TERM_version 2008-10-22 00:12:00 TERM / TERM_version
genbank2bsml / current 2009-03-30 13:34:00 genbank2bsml / current
genbank2bsml / current 2009-05-13 17:26:00 pAPEC-1 Conversion
genbank2bsml / current 2009-05-15 16:54:00 genbank2bsml / current
genbank2bsml / current 2009-05-18 17:34:00 pVM01 conversion BSML
genbank2bsml / current 2009-05-20 13:44:00 APEC related plasmids entry/BSML conv
sybil web site: sybil.sourceforge.net e-mail: nolanlabadmin@iastate.edu