The Genome Viewer

Introduction

The Genome Viewer (also known as the SEED Viewer) is our window into the various genetic data bases on the NMPDR Website. It comes in two slightly different flavors.

The NMPDR logo and banner (above left) appears when you are working with the Sprout Database, which contains curated data on mostly-complete genomes. When you are working on data in progress, you get the SEED logo and banner (above right).

SeedViewing.png
You'll see the SEED logo on the MG-RAST Server and the RAST Server. (You'll also see it at the Annotation Clearinghouse, but in that case it's not the Genome Viewer, it's the clearinghouse editor.) While you're using the RAST servers, you're looking at a combination of your own data and the publicly-available genome data in an NMPDR database, as shown in the diagram to the right.

A sample Genome Viewer page is shown below. Directly under the banner is a menu bar for navigation. On most pages, the top section contains an overview of information about the object being viewed (in this case, a feature). The bottom section contains graphical information such as pie charts or a browsable genome map. In most cases, there will be two tabs in this area. The Visual tab contains the graphic, and the Tabular tab contains the same information in an Interactive Table suitable for sorting, filtering, and downloading.

Seed Viewer page example

Topics

  • Compare Regions The Compare Regions Display The compare regions display is the signature visual tool of the NMPDR GenomeViewer. The purpose of the display is to show the chromosome ...
  • Genome Viewer Annotation Page Annotation Overview Page The Annotation page shows a variaty of information about a single feature . The page is roughly divided into three parts. The Annotation ...
  • Interactive Table Interactive tables easily recognizable because of their powder blue column headers can be found in various places all over the NmpdrWebsite. The example shown below ...
  • Linking to the Genome Viewer We support linking to the GenomeViewer using a generic mechanism via the base URL The linkin.cgi script provides a short, unified mechanism for getting into ...
SequencingForm
Sequence 000400
Summary Instructions for using our genomic data portal
Topic revision: r14 - 25 Dec 2008 - 06:01:13 - Bruce Parrello
FIG.GenomeViewer moved from FIG.SeedViewer on 18 Aug 2008 - 15:31 by Bruce Parrello - put it back
 
Notice to NMPDR Users - The NMPDR BRC contract has ended and bacterial data from NMPDR has been transferred to PATRIC (http://www.patricbrc.org), a new consolidated BRC for all NIAID category A-C priority pathogenic bacteria. NMPDR was a collaboration among researchers from the Computation Institute of the University of Chicago, the Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, and the National Center for Supercomputing Applications (NCSA) at the University of Illinois. NMPDR is funded by the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, under Contract HHSN266200400042C. Banner images are copyright © Dennis Kunkel.