Download Technical document The purpose of this document is to help

Technical document
The purpose of this document is to help navigate through the major features of this website and act
as a basic training manual to enable you to interpret and use the resources and tools involved the
annotation of the B. rapa BACs. It will also cover using other resources found on this website such
as the Brassica 95K microarray database and the local blast server.
These issues will be addressed by running through a real example.
Section 1 – Using the website to investigate a specific B. rapa BAC.
There are 3 different ways you can search for a BAC on the website, these are,
1. Using the link to display all the BACs. This will instantiate a pop-up window that displays
all the BACs that are “currently” available in the database. From there, you can scroll
through the list and click on the name of the BAC of your choice, which will in turn, direct
you to the Gbrowse annotation display for that clone.
2. Using the link to display the most recently annotated BACs. Again this works in the same
way as the above, only this link will display the BACs that have been added to the database
in the last 31 days.
3. Using the “BAC name search” search box. In this box you can type the name of the BAC.
The term you enter is then used to search the database and come up with any results that
match your entry in the form of a pop-up window, from there you can click on the BAC of
your choice and that will take you to the annotation page of that BAC. The search is case
insensitive and wild cards are enabled, so, for example, if you wanted to to retrieve all
KBrH BACs, then you can simply type that in the search box and all the KBrH library
BACs will be displayed.
Type KBrB123I09 in the search box and follow the link from the pop-up window to the
annotation page for that BAC by clicking on the BAC name itself.
This will display the annotation page for this BAC. By default, the tracks that are enabled are,
a. The PASA gene model alignments.
b. The A. thaliana gene model alignments.
c. Brassica EST transcript assembly alignments.
You can use your mouse to hover over one of the PASA gene models, this will initiate a tooltip
displaying information about that gene model and a link (“show virtual protein sequence”) of that
gene model. Clicking on this link will initiate another display that displays information about the
individual CDS features of the predicted gene. At the top of this display, you can find a button
“Start Jalview”, which will instantiate a jalview alignment pop-up display. You can use the jalview
display to scroll through the alignment of the gene model and visually inspect it.
If you scroll down to the bottom of the main Gbrowse annotation display of the BAC, you can see
all the different annotation tracks that are available, these are grouped into 6 major categories, they
are,
a. Overview.
b. Analysis.
c. Gene Predictions.
d. General.
e. Markers.
f. Transcript assemblies.
You can select to display any of the tracks that you are interested in by “checking” the
corresponding tick box and clicking on “Update image”.
Clicking on the title of the track will open a new page that displays more detailed information
describing what that track actually is.
There are various different ways in which you can manipulate the display of the BAC annotation,
but this document will not be covering them, a more detailed tutorial on how to use the Gbrowse
display can be found here.
The “Landmark or Region” search box in the Gbrowse annotation page can be used to extensively
search the BAC database. You can use it to search for BACs, Arabidopsis gene models that are
aligned to the rapa BACs, EST transcripts etc... Essentially, you can use this search box to search
for any information about the different tracks or the BACs, or even by using keyword searches.
Have a look at the examples section in the annotation page.
The sections that were explained above cover a main “walk-through” of how to use the site to
investigate B. rapa BAC annotations. You should now navigate back to the homepage of the project
http://brassica.bbsrc.ac.uk to continue with this tutorial.
Section 2 – local Blast server and Blastable databases.
We will now look at the local blast server hosted on this site. You can find this local blast
implementation by following the “Brassica Blast Server” link on the main page. This will initiate a
pop-up window, which can be used to blast your sequence against the following databases,
1. Sequenced KBr BACs.
2. JBnB (B. napus) BACend sequences.
3. KBr (B. rapa) BACend sequences.
4. All BrassicaDB sequences
5. EST assemblies (95K unigenes)
6. BrassicaDB-protein.
7. Arabidopsis pseudochromosomes.
8. Arabidopsis genes.
9. B. oleracea GSSs.
A blast search is also implemented explicitly on the Brassica 95K unigene set and this will blast
your sequence against all the unigenes that went into implementing the Brassica 95K microarray
(more information about the Brassica microarray can be found at ????). Following the “blast vs
unigenes” link will display a pop-up window of the blast submission form similar to the previous
example.
There is also a database, which holds information about the unigenes that went into the making of
the microarray and a guide on how to interrogate the database. This guide is available by following
the “Read me” link in the Brassica 95K unigene section of the main page.
An ftp site is also available where various data files relating to the project can be found. You can
also look at the “README” file on the ftp site to understand what information all the different files
on the ftp site contain. The link to the ftp site is available on the main homepage.