Bluejay for the Impatient
Table of Contents
Step 1 - Bookmarks and a first glance...
Step 2 - Zooming in for more information
Step 3 - The Context Tree
Step 4 - Navigation ("go-to")
Step 5 - Navigation (helpful keyboard shortcuts
to make navigation easier)
Step 6 - Looking at the data with a different
view...
Step 7 - Hyperlinks in the document...
Step 8 - Viewing the data "behind the scenes"
Step 9 - Saving the graphics to be printed later...
Step 10 - More views to consider...
Step 11 - A different orientation...
Step 12 - Looking at the other strand...
Step 13 - Limiting what you want to see...
Step 14 - Setting window preferences...
Step 15 - Take notes!
Step 1 - Bookmarks and a first glance...
Go to the menu Bookmarks -> Guillardia theta. Wait for the
image to appear. Notice that the browser logo bluejay
bobs on the branch while the document is loaded. What you
have is a graphical representation of a complete Guillardia genome.
Look at the Legend on the bottom left side of the screen.
See if you can locate the different encoding regions on the genome
by color. Then click or unclick different genes to show / hide
them in the main window.
For more about the Legend, search for it in the Help Browser (Help
-> Help Browser).
Step 2 - Zooming
in for more information
On the top right hand side of the screen is a zoom mechanism.
Play with the zoom to select the desired size of the image.
How much detail can you see?
For more about the Zoom feature, search for it in the Help Browser
(Help -> Help Browser).
Step 3 - The
Context Tree
Go to the Context Tree (found on the left side, top half of screen).
Check or uncheck a box there and click on Apply. Notice
how the contents of the main window change to display or hide the parts
you have checked / unchecked. For more information on how the Context
Tree works, search for "Context" in the Help Browser search tool.
Step 4 -
Navigation ("go-to")
Zoom into the image somewhat. Now, on the lower left side
of the screen is the Tabbed Panel. Select the Navigation
tab.
Enter in a specific base pair position in the sequence, or use the slider
to select a base pair to "go to". Notice that the main window image
reloads to show the sequence section that surrounds the chosen position.
Step 5 - Navigation (helpful
keyboard shortcuts to make navigation easier)
See the Navigation Page for more information
on Navigation shortcuts.
Step 6 - Looking
at the data with a different view...
Play with the different views a bit. See what the Pie
Chart, Two-Frame, Six-Frame, and Text view modes do to the image
displayed.
Step 7 - Hyperlinks
in the document...
Now reset the view to Two-Frame, if it isn't already in this
view. Click on one of the genes in the sequence. Notice that
a list of links come up. The first link is one to the corresponding
Magpie web page for this gene (if available). The other items in the
list (if there), are BioMOBY Services. In short, BioMOBY services display
extra information inherent in the data set for this gene. For more
information on BioMOBY, search for it in the Help Browser.
Step 8 -
Viewing the data "behind the scenes"
Go to the menu Document -> View Raw Data. The newly
opened window shows the raw data in BIOML format, which is a kind of
XML.
It describes the structure of the Guillardia genome using markup
language (tags). The file is organized as nested tags.
For more about this feature, search for it in the Help Browser (Help
-> Help Browser).
Step 9 - Saving
the graphics to be printed later..
Go to menu Document -> Convert Image to SVG. Then select
"Current Screen". You will next be prompted to enter in a file name
and a location to save the SVG file as. (for more information on what
SVG is, see The W3C website.
The resulting file will be a high-quality image that can be then manipulated
in imaging software that supports the format (such as CorelDraw). For
more about this feature, search for it in the Help Browser (Help ->
Help Browser).
Step 10 - More views to consider...
Go to menu View -> Shape Tab
Select linear and then click Apply. What you
have now is a linear representation of the Guillardia genome.
For more about this feature, search for it in the Help Browser
(Help -> Help Browser).
Step 11 - A
different orientation...
First, make sure you are back to a circular view. It should make sense
that a linear genome would not significantly benefit from rotation. Then,
go to menu View -> Orientation Tab.
Select Rotate and change the degrees box to 45. The
Guillardia genome has now been rotated 45 degrees clockwise.
For more about this feature, search for it in the Help Browser (Help
-> Help Browser).
Step 12 - Looking at the other strand...
In the Orientation Tab, select the Rev. Comp. (Reverse
Complement). Click on Apply. Notice that the complementary
DNA strand has now been reversed and has traded places with the original
strand.
For more about this feature, search for it in the Help Browser (Help
-> Help Browser).
Step 13
- Limiting what you want to see...
In the Orientation Tab, select the Cut option. Slide
the ruler over to, say, 500 and click Apply. Use the Navigation
Tab and mouse zoom features to see that the top left of the linear
view has shifted and now starts at the base value inputted.
For more about this feature, search for it in the Help Browser (Help
-> Help Browser).
Step 14 -
Setting window preferences...
Go to menu Program -> Drawing Prefs. Play with
the color schemes there to customize your display windows.
Step 15
- Take notes!
Enter some notes into the Notes tab.
See that they remain there with the document.
For more about this feature, search for it in the Help Browser (Help
-> Help Browser).
Now you're ready!
Hopefully this quick little tour has shown you some of the highlights
of Bluejay in an interactive and guided manner. If you require more
information on any of the features covered in this brief overview, please
see the Help Browser (Help -> Help Browser).