The Genome Viewer

Introduction
Topics

Introduction

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

The NMPDR logo and banner (shown at 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 (shown at right).

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 Seed 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 a table suitable for sorting, filtering, and downloading.

Topics

LinkingToTheGenomeViewer 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: r11 - 28 Aug 2008 - 22:16:49 - BruceParrello

FIG.GenomeViewer moved from FIG.SeedViewer on 18 Aug 2008 - 15:31 by BruceParrello - put it back

NMPDR is 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.