DEDB :: Drosophila melanogaster Exon Database
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DEDB

9 January 2006 - Database has been updated to FlyBase Genome Annotation Version 4.2.1.

9 July 2004 - Help pages have been added describing the process of linking to and from FlyBase.

8 July 2004 - FlyBase gene records now have links to DEDB's Splicing Graph Viewer in the "External database links" section. Click here for an example.

1 July 2004 - Updated methodology page with detailed information and examples on the classification of alternative splicing events. There is a new help page that describes in detail the Splicing Graph Viewer. The Python module for drawing the splicing graphs is available in the downloads page.

14 May 2004 - DEDB updated to FlyBase genome annotation release 3.2

Introduction

Drosophila melanogaster Exon Database (DEDB) is a database that contains information on Drosophila melanogaster exons presented in a splicing graph form. The data in this database is based on release 3.2 of the Drosophila melanogaster genome annotations available at FlyBase (www.flybase.net). The gene structure information extracted from the annotations were checked, clustered and transformed into splicing graph. The splicing graph form of the gene constructs were then used for classification of the various types of alternative splicing events. In addition, Pfam domains were mapped onto the gene structure.

Query

Users can query the database using the query page using BLAST, FlyBase Gene Name, FlyBase Gene Symbol, Pfam Accession Number and Pfam Identifier. This allows users to determine the Drosophila melanogaster homology of their gene using a BLAST search and to visualize the alternative splicing variants if any. Users can also determine genes containing a particular domain using the Pfam Accession Numbers and Identifiers.

Downloads

All the splicing graphs are available for download as XML files on the downloads page.

Splicing Graph Viewer

To visualize the splicing graph construct, a Splicing Graph Viewer is available. This allows for the presentation of all the various forms of alternative splice variants in an easy to understand graph.


An example of a splicing graph

Alternative splicing event classification

The following forms of alternative splicing events are used in the classification:

  • Alternative initiation exon
  • Alternative termination exon
  • Alternative transcriptional start site
  • Alternative transcriptional termination site
  • Alternative donor site
  • Alternative acceptor site
  • Cassette exon
  • Intron retention

Click here for the details.

Methodology

Details of the methods used in the construction of DEDB are found in the methodology page.

Contacts

Prof. Shoba Ranganathan
Assoc. Prof. Tan Tin Wee
Lee Teck Kwong Bernett