Seqpare

Seqpare quantifies similarity between genomic interval sets by computing a single-index metric equal to the ratio of their effective overlap to their union, enabling consistent comparison of interval sets produced by sequencing methods.

Key Features:

• Self-consistent similarity metric: Calculates a self-consistent index for comparing genomic interval sets.
• Single-index output: Produces one similarity value per pair of interval sets equal to the ratio of effective overlap over their union.
• Interpretability: The similarity index ranges from 0 (no overlap/unrelated) to 1 (identical interval sets).
• Effective overlap focus: Quantifies similarity by summing total effective overlaps between interval sets.
• Search and mapping functions: Implements searching and mapping operations on large genomic interval datasets.
• Implementation base: Built upon the foundational code base ailist.

Scientific Applications:

• Pairwise interval comparison: Quantify similarity between two genomic interval sets derived from sequencing experiments.
• Large-scale dataset comparison: Compare and rank similarity across large collections of interval sets for genomics analyses.
• Interval search and mapping: Locate and map overlapping intervals within extensive genomic interval datasets.

Methodology:

Computes a similarity index by evaluating the total effective overlap between two interval sets relative to their union and implements searching and mapping functions; implemented on the ailist code base.