OLego

OLego maps RNA-seq reads to genomes to enable sensitive detection of splice junctions and micro-exons in mammalian transcriptomes.

Key Features:

• Multiple-Seed-and-Extend Scheme: Uses small seeds (~14 nt) tailored for mammalian genomes to increase sensitivity for splice junction detection.
• Built-in Statistical Model: Scores exon junctions based on splice-site strength and intron size to improve mapping accuracy and resolve junction ambiguities.
• Efficient Mapping with BWT: Employs the Burrows-Wheeler Transform (BWT) in multiple algorithmic steps to map seeds, locate junctions, and identify small exons.
• Multithreaded Execution: Implemented in C++ with full multithreading to enable rapid processing of large RNA-seq datasets.

Scientific Applications:

• Benchmarking: Demonstrated improved sensitivity, comparable or higher accuracy, and significantly increased speed on simulated and real RNA-seq datasets.
• Micro-exon discovery: Identified hundreds of novel micro-exons (less than 30 nt) in the mouse transcriptome, many of which are phylogenetically conserved and experimentally validated in vivo.

Methodology:

Uses small (~14 nt) seeds, a statistical model scoring junctions by splice-site strength and intron size, applies the Burrows-Wheeler Transform across mapping and junction-identification steps, and is implemented as a multithreaded C++ program.