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Open Access Database

DEDB: a database of Drosophila melanogaster exons in splicing graph form

Bernett TK Lee1, Tin Wee Tan1 and Shoba Ranganathan12*

Author Affiliations

1 Department of Biochemistry, National University of Singapore, Singapore

2 Biotechnology Research Institute, Macquarie University, Sydney, Australia

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BMC Bioinformatics 2004, 5:189  doi:10.1186/1471-2105-5-189

Published: 7 December 2004

Abstract

Background

A wealth of quality genomic and mRNA/EST sequences in recent years has provided the data required for large-scale genome-wide analysis of alternative splicing. We have capitalized on this by constructing a database that contains alternative splicing information organized as splicing graphs, where all transcripts arising from a single gene are collected, organized and classified. The splicing graph then serves as the basis for the classification of the various types of alternative splicing events.

Description

DEDB http://proline.bic.nus.edu.sg/dedb/index.html webcite is a database of Drosophila melanogaster exons obtained from FlyBase arranged in a splicing graph form that permits the creation of simple rules allowing for the classification of alternative splicing events. Pfam domains were also mapped onto the protein sequences allowing users to access the impact of alternative splicing events on domain organization.

Conclusions

DEDB's catalogue of splicing graphs facilitates genome-wide classification of alternative splicing events for genome analysis. The splicing graph viewer brings together genome, transcript, protein and domain information to facilitate biologists in understanding the implications of alternative splicing.