User tutorial for the Sol Genomics Network

For New Users

Objective:

A database is a place where any kind of information (data) is stored, usually information that is related in some way. SGN is a database containing information about a group of related plants, including tomato, potato, eggplant, pepper, petunia and coffee. The information stored here includes data about these plants that scientists around the world can use in their research. In addition, SGN contains tools such as certain software programs that help scientists use the data, for example to compare genetic information from one plant species to another. So databases are not only for storing information, but also for sharing and using it. The purpose of this tutorial is to show you some examples of how this works.

This tutorial can be used as a self-tutorial or as a guided class. It requires a basic level of biology (understanding terms such as DNA, gene, species, etc.) and the ability to use an internet browser. By the end of this tutorial you should understanding what types of information can be stored in a biological database, how scientists can access and use this information, and how these databases are used by scientists.

Background information:

DNA (Deoxyribonucleic acid) is the molecule that encodes the genetic information which is passed from one generation to the next. DNA is a double-stranded molecule held together by bonds between pairs of nucleotides. The four nucleotides in DNA contain the bases adenine (A), guanine (G), cytosine (C), and thymine (T). Due to their chemical structure, base pairs form only between A and T and between G and C; thus the base sequence of one DNA strand can be deduced from that of its partner. Therefore, a DNA sequence is simply given as a string of Gs, Cs, Ts, and As (for example, GACTTACG etc.).

An EST, expressed sequence tag, is a short DNA sequence (generally around 300-600 bases long) that is usually part of a gene. These are the most widely available type of DNA sequence for most organisms as they are easier and less expensive to produce than whole (genomic) DNA sequence.

For more detailed background information (and great pictures), see http://publications.nigms.nih.gov/genetics/, the Genetic basics site from the National Institute of Health, and http://www.ncbi.nlm.nih.gov/About/primer/index.html, a Science Primer from the National Center for Biotechnology Information.

How to use this tutorial:

The necessary steps to work through this tutorial are in Bold type. Questions you should be able to answer from the site are in Italics. You can either print this tutorial out first, or open the database in a new window, side by side with the tutorial.

Let’s begin!

Open http://www.sgn.cornell.edu , the Sol Genomics Network.

As mentioned, this site houses data for tomato and related plants such as potato, pepper, eggplant, petunia and coffee. Even on the home page, you can see that there is a lot of information available, including general information about this group of plants (for example, click on “What are Solanaceae?”), a newsletter for scientists interested in this project, upcoming meetings, but also very specific higher-level scientific information that is only relevant (or even understandable!) to scientists deeply involved in this type of research.

If you were a university student or scientist interested in using this database, it would most likely be because you had some prior information about a particular DNA sequence (perhaps you read about it in a scientific paper), or you had done a search on a particular subject and found related genes (for example, genes related to cell division). For this exercise, let’s say you read about some interesting DNA sequences and wanted to find out more about one or more of them. The names of several DNA sequences are below to use as examples. (Note that when scientists first start looking at a particular DNA sequence, in the beginning they often have no idea what type of gene it is from or anything about it. Therefore DNA sequences are either assigned some random name or number, or some code name that relates the DNA sequence to a particular project or even a particular place in the storage freezer!).

SGN-E481065

cLEX-13-G5

cLEN-17-L18

cLEI-2-j7

cLEF-49-i8

In the “search” box at the top of the page type in (or copy and paste) one EST name. The position of the hyphens are important.

You should see a page with a DNA sequence on it (a long string of Gs, As, Cs, Ts).

            Can you tell what kind of organism (species) of plant DNA sequence is from?

                        [note: this will be in botanical format, genus and species]

                        For example: Solanum lycopersicum is the scientific name for tomato, Solanum tuberosum for potato

            Can you find what kind of plant tissue it was from?

                        For example, root, tuber (in potatoes), seedling, fruit pericarp (the fleshy part of the tomato).

            Can you find what the length of your DNA sequence is?

                        Remember we said that a DNA sequence is a string of G,C,A,Ts. The length of a particular sequence  is given as base pairs (bp).

Now we know a little bit about this particular DNA sequence, where it came from, how long it is. But we might also want to know if there is any information available about what kind of gene it is from (what is its function in the plant?). For this there is a software program called BLAST = the Basic Local Alignment Search Tool, which compares your DNA sequence to all others in the database.

Click on the word “blast” underneath your DNA sequence. On the next page that comes up, change the “database” to “all SGN ESTS”, then click on Search. (For scientists very familiar with this program, there are certain parameters that can be changed if desired).

Scroll down past the colored graphs that come up on the top of the page (these are just overview summaries of the information, which is interesting to certain users). You should see:

>Sequences producing significant alignments:

These are sequences in the database showing similarity to yours, in order of most alike to least like. Below is the comparison between your sequence (query) and each of the other sequences (subject). You can see that there are places where the 2 sequences don’t match completely.

Go back to the Blast page and change the Database selection to one of the protein databases instead.

What kind of gene is your sequence most similar to?

For example, these might be things like: ripening related protein, cell division proteins, pathogenesis (disease) related, etc. Frequently, these are unknown! There is still a lot of things left for scientists to discover!

You should be able to understand now how useful this information could be to a plant scientist. Starting with just a little bit of information, you were able to find out a lot more. This is why these biological databases are so important to scientific research.

For more information or any questions, please contact Theresa Fulton at tf12@cornell.edu