An explanation of the Distributed Annotation System (DAS) with a worked example of how to attach an RNA-Seq DAS source to the VectorBase genome browser.

1. VectorBase
DAS at VectorBase
February 2010
Karyn Mégy - February 2010

2. VectorBase Plan
• In this tutorial you will find:
- A brief introduction to DAS
> What is it? Why using it? What is the concept?
- A step by step guide on how to install a DAS track
> Example of the Anopheles RNA-Seq
Karyn Mégy - February 2010 2

3. VectorBase
Introduction
What is DAS? Why using DAS?
What is the concept?
Karyn Mégy - February 2010 3

4. VectorBase Distributed Annotation
System
• Developed by Robin Dowell, Sean Eddy and Lincoln Stein
• Specification of a protocol for requesting and returning sequence and
annotation data
• Allows decentralised storage of sequence annotation and integration on
demand basis by client-side software
• Simple storage protocol running over HTTP
…. see http://biodas.org for more details.
Karyn Mégy - February 2010 4

5. VectorBase Why DAS?
• Annotation easier to share
• Annotation can be stored in a variety of formats
• Control over updating the data left to the original data provider
• Conflicting annotation permitted
Karyn Mégy - February 2010 5

6. VectorBase DAS concept
Annotation server A Annotation server B Annotation server C
E.g. manual annotation E.g. ESTs clusters E.g. RNA-Seq data
@ VectorBase @Mexico @ EBI
Annotations
- URL
- Upload a file
Reference
Sequence on which
to align the annotations
Client Reference server
@ VectorBase @ VectorBase
Karyn Mégy - February 2010 6

7. VectorBase DAS concept
Annotation server A Annotation server B Annotation server C
E.g. manual annotation E.g. ESTs clusters E.g. RNA-Seq data
@ VectorBase @Mexico @ EBI
Annotation server C
Annotations
- URL
- Upload a file
Reference
Sequence on which
to align the annotations
Client Reference server
@ VectorBase @ VectorBase
Karyn Mégy - February 2010 6

8. VectorBase DAS concept
Annotation server A Annotation server B Annotation server C
E.g. manual annotation E.g. ESTs clusters E.g. RNA-Seq data
@ VectorBase @Mexico @ EBI
Annotation server C
Annotations
- URL
- Upload a file
Reference
Sequence on which
to align the annotations
Client Reference server
Reference server
@ VectorBase @ VectorBase
Karyn Mégy - February 2010 6

9. VectorBase DAS concept
Annotation server A Annotation server B Annotation server C
E.g. manual annotation E.g. ESTs clusters E.g. RNA-Seq data
@ VectorBase @Mexico @ EBI
Annotation server C
Annotations
- URL
- Upload a file
Reference
Sequence on which
to align the annotations
Client
Client Reference server
Reference server
@ VectorBase @ VectorBase
Karyn Mégy - February 2010 6

10. VectorBase Client/Server
• Client: an application (e.g. Apollo) or a website (e.g. VectorBase)
requesting and displaying annotation for a region of a sequence
• Server: a reference server (provide the sequence) or an annotation server
(provide the annotations) that has the knowledge about the sequence and/
or annotation data stored in a flat file or a database
-> DAS server implementation
• LDAS
http://www.biodas.org/servers
- The lightweight DAS server using Perl, Apache and MySQL
• DAZZLE
http://www.derkholm/thomas/dazzle
- DAS server written in Java
• ProServer
http://www.sanger.ac.uk/proserver
- DAS server written in Perl
Karyn Mégy - February 2010 7

11. VectorBase
How to set up a DAS track,
Example of the Anopheles RNA-Seq data
Karyn Mégy - February 2010 8

12. VectorBase Setting up a DAS track
• Open the « DAS Sources» menu in the genome browser
• Select « Manage sources » a new window will open
Karyn Mégy - February 2010 9

13. VectorBase Setting up a DAS track
• If your server is not already here, select « Add Data Source »
! You might have to wait up to 30 sec. before seeing the next screen, so be patient !
Karyn Mégy - February 2010 10

14. VectorBase Setting up a DAS track
• If your source is not listed, • If your source is listed,
• Enter your server address in • Select it, click on « Next »
the « Name/URL/Description » box, (and skip the next slide)
and click « Apply »
e.g. for the RNA-Seq data: http://www.ebi.ac.uk/das-srv/ensemblgenomes
Sources
Karyn Mégy - February 2010 11

15. VectorBase Setting up a DAS track
• Choose your annotation track from the list, and click « Next »
! You might to wait 30 sec. before seeing the next screen , so be patient !
Karyn Mégy - February 2010 12

16. VectorBase Setting up a DAS track
• Choose where the mapping will • Enable on whichever pages are
show. relevant
Usually « Ensembl top level» gives E.g. ContigView and GeneView
best results, however if you’ve aligned for the RNA-Seq
your sequences to a different coordinate
system (e.g. individual clones) you
might want to have another option.
Karyn Mégy - February 2010 13

17. VectorBase Setting up a DAS track
• Set the display mode for the track, Click on « Finish »
Default settings are usually OK.
e.g. of the RNA-Seq: rename to a shorter name, chose « Tilling array » as chart
Karyn Mégy - February 2010 14

18. VectorBase Setting up a DAS track
• Your DAS track should now appear in the DAS sources list,
• Click on « close » (this will close the window)
Karyn Mégy - February 2010 15

19. VectorBase Setting up a DAS track
• Your DAS track should now appear in the browser.
Karyn Mégy - February 2010 16

20. VectorBase
Questions?
Karyn Mégy - February 2010 17

21. VectorBase Help !
• More about DAS (specially to set up a DAS server):
• Ensembl documentation:
http://www.ensembl.org/info/docs/das/das_server.html
• Sanger documentation:
http://www.sanger.ac.uk/resources/software/das/
Karyn Mégy - February 2010 18

22. VectorBase Help !
• E-mail VectorBase at info@vectorbase.org
• Post a question on the forum
http://www.vectorbase.org/sections/Forum/index.php
• Check out the FAQs
http://www.vectorbase.org/Help/Help:Contents
Karyn Mégy - February 2010