JOA

JOA performs genomic interval intersection across multiple genomic-interval sets to identify overlapping intervals from next-generation sequencing (NGS) data without requiring pre-sorted input or prohibiting nested intervals.

Key Features:

• Unconstrained Interval Intersection: Performs intersections without constraints on nesting or input sorting.
• Segment Tree (ST): Implements a segment tree (ST) data structure to efficiently find overlapping intervals.
• Indexed Segment Tree Forest (ISTF): Implements an indexed segment tree forest (ISTF) that augments the segment tree with indexing and natural binning to enable more efficient parallel interval intersection.
• Parallel Processing: Leverages Java's fork/join framework to parallelize processing across available processor cores.
• Performance and Scalability: Comparative analyses demonstrate that ST and ISTF are comparable in execution time and memory usage, and that runtime decreases with increased processor availability.

Scientific Applications:

• Comparative Genomics: Enables intersection of multiple genomic interval sets for comparative genomics analyses.
• Functional Genomics: Supports combining interval datasets for functional genomics studies.
• Epigenomics: Facilitates intersection of large-scale epigenomic interval sets derived from NGS data.

Methodology:

Uses segment tree and indexed segment tree forest data structures with indexing and natural binning, and parallelizes computations using Java's fork/join framework to intersect nested and unsorted genomic intervals.