Kassiopeia

Kassiopeia predicts and stores genome-wide mutually exclusive exon (MXE) candidates to support analysis of mutually exclusive splicing and its impact on protein isoform diversity.

Key Features:

• MXE prediction criteria: Predicts MXEs based on similar exon lengths, sequence homology, conserved splice sites, and translation within the same reading frame.
• Scipio-based gene reconstruction: Performs gene reconstructions using the Scipio algorithm, with an 83.5% reconstruction rate for annotated MXEs in Drosophila melanogaster.
• Species coverage: Provides MXE predictions across twelve Drosophila species, Arabidopsis thaliana, Caenorhabditis elegans, and humans.
• Search and parameterization: Supports BLAST-based queries and gene browsing with adjustable prediction parameters to explore divergent and highly similar exon candidates.
• Gene structure and sequence outputs: Outputs detailed gene structure schemes including exon sequences and predicted RNA secondary structures of MXEs.
• Evidence integration: Integrates cDNA/EST evidence, homology-based predictions from closely related species, and RNA secondary structure predictions to support MXE identification.
• Generation and storage: Generates and stores genome-wide analyses of mutually exclusive exomes for downstream analysis.

Scientific Applications:

• Alternative splicing mechanism analysis: Investigating mutually exclusive splicing mechanisms and their sequence- and structure-based determinants.
• Comparative genomics of MXEs: Comparative identification and evolutionary analysis of MXEs across model organisms including Drosophila species, Arabidopsis thaliana, Caenorhabditis elegans, and humans.
• Gene annotation and validation: Supporting annotation and validation of MXEs in gene models using Scipio reconstructions and cDNA/EST evidence.
• Protein isoform diversity inference: Inferring potential protein isoform diversity resulting from mutually exclusive exon usage.

Methodology:

Uses Scipio for gene reconstructions; predicts MXEs by applying criteria of similar exon lengths, sequence homology, conserved splice sites, and translation in the same reading frame; integrates cDNA/EST evidence, homology-based predictions from related species, and RNA secondary structure predictions; and supports BLAST queries and adjustable prediction parameters.