SplitSeek

SplitSeek predicts de novo splice junctions and detects chimeric transcripts from short-read RNA-seq data to identify novel splicing events and report genomic rearrangements.

Key Features:

• De Novo Prediction Capability: Predicts splice junctions without relying on existing annotations, enabling discovery in unannotated regions or species with incomplete reference genomes.
• Detection of Novel Splicing Events: Identifies novel splicing events that are not captured by traditional annotation-based methods.
• Identification of Chimeric Transcripts: Detects chimeric transcripts formed by fusion of exons from different genes.
• Genomic Rearrangement Reporting: Reports genomic rearrangements including insertions and deletions and other structural variations.

Scientific Applications:

• Gene Expression Studies: Enables analysis of alternative splicing mechanisms by identifying novel splice events.
• Cancer Research: Facilitates detection of chimeric transcripts for identification of potential oncogenic fusions.
• Genomic Structural Variation Analysis: Supports studies of genomic stability and evolution by reporting insertions, deletions, and rearrangements.

Methodology:

SplitSeek leverages short-read RNA-seq data to predict splice junctions; when tested on mouse RNA-seq datasets it predicted over 31,000 splice events, with 88% bridging regions separated by ≤100 kb and 74% connecting exons within the same RefSeq gene.