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Searching genomic interval sets produced by sequencing methods has been widely and routinely performed; however, existing metrics for quantifying similarities among interval sets are inconsistent. Here we introduce  Seqpare,  a self-consistent and effective metric of similarity and tool for comparing sequences based on their interval sets. With this metric, the similarity of two interval sets is quantified by a single index, the ratio of their effective overlap over the union: an index of  zero  indicates unrelated interval sets, and an index of  one  means that the interval sets are identical. Analysis and tests confirm the effectiveness and self-consistency of the  Seqpare  metric.

Seqpare: a self-consistent metric of similarity between genomic interval sets