PlantGDB BLAST - Introductory Tutorial
This step-by-step tutorial covers the basic operations of the PlantGDB BLAST tool.
Step 1. Getting started
The above picture is the first thing you're likely to see when you open the PlantGDB BLAST webpage in your web browser. Featured are complete genome databases of some very common species. On the column next to it, is a box for other databases that might be of interest to the majority of our users. If you're not looking for these species, don't despair, our tool is designed to fit your needs!
Select the checkbox next to the organism you might want to search. You can select multiple organisms.
Step 2. The "All" shortcut buttons
The above four buttons are shortcut buttons for datasets that otherwise might require you to select many organisms. The "All" buttons will select all of the available data in our database of that type. The behind the scenes operations of these buttons involves the maintainence of a vast database of species which are systematically identified and classified into groups. By selecting one of these groups, all of the data belonging to that group is included in your search.
As you might have noticed, upon clicking any one of the "All" buttons, that group appears in another table on the webpage with multiple checkboxes next to it, prompting you to select the type of genomic data or mRNA data you would like to use in your search of that group.
Part of this new system, is flexibility in your search query. As you can see above, you can select any combination of datatype to make them the target of your BLAST search. Another useful option is the All DNA Seqs. button, which when clicked will select all types of data for that particular species.
An indicative feature of the behind the scenes work being done, is a grey colored bar, that reads "Searching..." to indicate that the species name you have typed, as you go, is being searched. The system uses whatever you have entered between keystrokes, as input, and fetches records starting with that name. In the example, the ulterior motive is to select Arabidopsis Thaliana. By typing Arabidopsis, we were able to get a list of sub species, and then click to choose the desired result.
You are now ready to put your query into the Query Textbox, and click the Run BLAST button at the end of the page.