VectorBase DAS Tutorial

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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.

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  • VectorBase DAS Tutorial

    1. 1. VectorBase DAS at VectorBase February 2010 Karyn Mégy - February 2010
    2. 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. 3. VectorBase Introduction What is DAS? Why using DAS? What is the concept? Karyn Mégy - February 2010 3
    4. 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. 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. 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. 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. 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. 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. 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. 11. VectorBase How to set up a DAS track, Example of the Anopheles RNA-Seq data Karyn Mégy - February 2010 8
    12. 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. 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. 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. 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. 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. 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. 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. 19. VectorBase Setting up a DAS track • Your DAS track should now appear in the browser. Karyn Mégy - February 2010 16
    20. 20. VectorBase Questions? Karyn Mégy - February 2010 17
    21. 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. 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

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