Abstract
BackgroundA 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.DescriptionDEDB 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.ConclusionsDEDB'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.
Highlights
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
The sequences displayed by clicking on the nodes in the splicing graph are always shown in the sense orientation to facilitate translation of coding sequences and Pfam mapping, while the exon and intron sequences shown by selecting genomic segments on the transcripts will retain their original orientation identified by chromosomal mapping
The classical approach is tedious in cases where the number of splice variants are numerous resulting in the user having to correlate large amounts of data to comprehend all the alternative splicing events taking place
Summary
The data housed in DEDB is organized as splicing graphs, which allows for ease of alternative splicing classifications. This has allowed DEDB to provide clean sets of data containing specific types of alternative splicing events. These specific sets of data could prove useful in understanding the biological basis of alternative splicing because different forms of alternative splicing have different biological basis. The splicing graph viewer provided allows biologists to quickly and intuitively understand the effects of alternative splicing on a gene of interest, aiding their research.
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