The Plant Genome Databases - A Tutorial

The databases covered in this tutorial can be a valuable tool for students and scientists from many different disciplines. The support for their creation and maintenance has been provided by the Plant Genome Research Program. Each database is developed and maintained by a different set of curators, located around the globe. A World Wide Web interface to these databases is provided as part of Demeter's Genome's at the USDA/ARS Center for Bioinformatics and Comparative Genomics (CBCG). This tutorial is based on that interface and uses the copies of the databases that reside on the AGIS computers. Each database group may, however, submit database-specific attachments, which describe other services offered, alternate versions of the database, and other unique aspects of a particular database. Be sure to check those out if you are a frequent user of these databases. Finally, the National Agricultural Library and the Plant Genome Data and Information Center provide additional resources that may be of interest to you.

Each database is focused on one or more species, and the information they contain may include genetic maps, molecular markers, germplasm characteristics, quantitative traits, DNA sequences, and much more. Each curatorial group may organize and present this information in a slightly different way, tailored to their organism and user community. Hopefully this tutorial will give you ideas on how to search the databases, where to look for the information you need, and how to interpret the displays.

The tutorial is divided into a series of lessons. You do not have to do the lessons in order, but many of them will build on skills learned in earlier lessons. At the top of each lesson there will be a Tools and Techniques section that identifies new skills that will be covered. The lessons also include examples from several different databases. The examples were created as part of this tutorial and are meant to showcase particular methods or displays, and you are strongly encouraged to look at these. If you are primarily interested in a single database or just want to check out the variety, you can browse through as many additional examples as you want.

The examples use a browser technique called "frames". Some older browsers don't support frames, in which case you will get an error message and you will need to update your browser software. When you follow an example, the lower window will contain a "live" connection into the genome database which you can use to execute the example, and the explanation and instructions will remain in the top window. You can change the relative sizes of the windows by dragging the bar dividing the two frames with your mouse. Some browsers will open the frame in a new instance of the browser - if your browser does this be sure to properly close (exit, don't just minimize) that instance when you're done with the example to avoid having many browser windows running.

Lesson 1 - Overview of Demeter's Genomes Home Page

Lesson 2 - Overview of Genetic Maps

Lesson 3 - Creating the Map

Lesson 4 - Points on Maps - genes/molecular markers

Lesson 5 - Intervals on Maps - cytological/introgressed regions

Lesson 6 - Intervals on Maps - rearranged/translocated regions/QTLs

Lesson 7 - Intervals on Maps - syntenic relationships

Lesson 8 - Physical Maps

Lesson 9 - Sequences

Lesson 10 - TableMaker - generating reports

Lesson 11 - Some practice questions

Lesson 12 - The native ACEDB interface

This is the end of the tutorial. Hopefully, you have a better idea of what these resources contain and how to use them. Return to the Plant Genome Data and Information Center Home Page