Alt Event Finder: a tool for extracting alternative splicing events from RNA-seq data

Area of Science:

• Genomics
• Molecular Biology
• Bioinformatics

Background:

• Alternative splicing generates diverse gene isoforms with varied functions.
• Identifying alternative splicing events is crucial for understanding transcript diversity and splicing regulation.

Purpose of the Study:

• To develop a computational tool for identifying novel alternative splicing events.
• To investigate changes in splicing patterns in response to external stimuli.

Main Methods:

• Developed Alt Event Finder, a tool utilizing genome-guided transcript annotation.
• Employed transcript reconstruction tools like Cufflinks and Scripture.
• Applied Alt Event Finder to RNA-seq data from rat liver tissues.

Main Results:

• Alt Event Finder successfully identified novel splicing events in the human genome.
• Discovered dozens of novel cassette exon events in rat liver tissue.
• Observed altered splicing patterns in response to extensive alcohol exposure.

Conclusions:

• Alt Event Finder effectively identifies de novo splicing events from data-driven transcript annotation.
• The tool is valuable for research into splicing regulation mechanisms.