SEED Viewer Manual

From TheSeed
Jump to: navigation, search

The SEED is a framework to support comparative analysis and annotation of genomes. The SEED Viewer allows you to explore the curated genomes that have been produced by a cooperative effort that includes Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, the University of Chicago and teams from a number of other institutions.

These pages will cover the usage of the different pages within the Seed Viewer.

An overview of the main pages in the SeedViewer can be found in the Contents Page.

Home

The home page of the seedviewer offers you several entry points to explore the data in the SEED.

Common components of a web page in the seedviewer are the following. The image below depicts the locations of the components:

(1) The menu

The menu is a green bar located under the SeedViewer Logo. Hovering over the menu will show you submenus that are relevant for the page you are viewing. The categories Navigate and Help will always be present on each page. Other menu categories are added dependent on the context of the page. Click here to learn more about using the menu.

(2) Find Window

On the right side of the menu bar you will find an input field with a find button in front of it. The Find Window allows you to search the SEED data for keywords or ids. To learn more about the search using the Find Window, click here.

(3) Login Box

For using the publicly available data in the SEED no login or registration is required. If you wish to use our services RAST or MG-RAST, you need to obtain a login. That way, we can ensure that only you have access to your private data. This is also very helpfull for feedback and support.

You can create a login by clicking on Register in the Help menu. To learn more about user management click here.

(4) Body of the Page

The home page allows you to specifically search the SEED data using five categories. They are presented in a TabView at the bottom of the Home page:

a) Organisms

Select an organism of interest in the Organism Select and press the button select. This will lead to the Organism Page of that organism.

b) Subsystems

Selecting a subsystem in the Select Box and clicking Select will lead you to a Subsystem Page. You can narrow the selection by typing in a part of the subsystem name into the field on top of the select box.

c) ID search

If you know the ID of a gene or protein you're interested in, you can directly specify it in this field and press ID Search. The ID can be a SEED (fig|...) ID as well as many other types of IDs from other databases (e.g. GenBank, KEGG, SwissProt, UniProt and others). These IDs are saved in the SEED as Aliases.

d) Text search

You can search for any type of data in this field. This includes search for Organisms, Subsystems, IDs as well as Functional Roles of proteins. It should be used carefully, as the search is an infix search and can take very long (e.g. if you only type in one letter it may take forever). If you already know that you are looking for, e.g. a subsystem, it would be faster to use the Subsystems tab.

e) BLAST

This tab offers the option to search a DNA or protein sequence against an organism in the SEED. It is described in more detail here.

Home1.png