Abstract
BackgroundAlternative splicing is an important process in higher eukaryotes that allows obtaining several transcripts from one gene. A specific case of alternative splicing is mutually exclusive splicing, in which exactly one exon out of a cluster of neighbouring exons is spliced into the mature transcript. Recently, a new algorithm for the prediction of these exons has been developed based on the preconditions that the exons of the cluster have similar lengths, sequence homology, and conserved splice sites, and that they are translated in the same reading frame.DescriptionIn this contribution we introduce Kassiopeia, a database and web application for the generation, storage, and presentation of genome-wide analyses of mutually exclusive exomes. Currently, Kassiopeia provides access to the mutually exclusive exomes of twelve Drosophila species, the thale cress Arabidopsis thaliana, the flatworm Caenorhabditis elegans, and human. Mutually exclusive spliced exons (MXEs) were predicted based on gene reconstructions from Scipio. Based on the standard prediction values, with which 83.5% of the annotated MXEs of Drosophila melanogaster were reconstructed, the exomes contain surprisingly more MXEs than previously supposed and identified. The user can search Kassiopeia using BLAST or browse the genes of each species optionally adjusting the parameters used for the prediction to reveal more divergent or only very similar exon candidates.ConclusionsWe developed a pipeline to predict MXEs in the genomes of several model organisms and a web interface, Kassiopeia, for their visualization. For each gene Kassiopeia provides a comprehensive gene structure scheme, the sequences and predicted secondary structures of the MXEs, and, if available, further evidence for MXE candidates from cDNA/EST data, predictions of MXEs in homologous genes of closely related species, and RNA secondary structure predictions. Kassiopeia can be accessed at http://www.motorprotein.de/kassiopeia.
Highlights
Alternative splicing is an important process in higher eukaryotes that allows obtaining several transcripts from one gene
In order to facilitate the production of datasets of mutually exclusive exomes and to provide a helpful interface for their analysis and presentation we have developed a web application, which we called Kassiopeia
Utility and discussion Here, we present the web application Kassiopeia that allows exploring the content of Mutually exclusive spliced exons (MXEs) in whole genomes
Summary
Exclusive splicing is a highly regulated mechanism leading to the inclusion of one exon of a cluster of neighbouring exons into the final transcript. We have set up a pipeline to predict MXE candidates in the whole genomes of several model organisms based on conserved splice sites, same reading frame, sequence similarity and similar length. To make these data accessible and informative, we constructed Kassiopeia, a web interface in which researchers can BLAST and search for specific proteins, or browse through whole genomes or chromosomes. KH and MK extensively tested the software, performed all analyses and wrote the manuscript. All authors read and approved the final version of the manuscript
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