MosaicLev: modified Levenshtein distance for mobile element-aware genome comparison.

IF 2.6 Q2 MATHEMATICAL & COMPUTATIONAL BIOLOGY

Bioinformatics advances Pub Date : 2026-09-07 eCollection Date: 2026-01-01 DOI:10.1093/bioadv/vbag261

Harry Stoltz, Thomas E Kuhlman

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Abstract

Motivation: Genomes diverge, in part due to the activity of mobile elements, including elements that excise and reinsert (cut-paste) or propagate via an RNA intermediate (copy-paste). Standard sequence comparison methods are not motif-aware, penalizing mobile element insertions based on length rather than recognizing them as single biological events, while alignment-free methods still fail to adequately describe a known mobile-element sequence as a unified change.

Results: We introduce a modified Levenshtein distance ( $mlev$ ) that discounts specified block insertions via a tunable parameter ( $m \in [0, 1]$ ): at $m = 0$ it recovers ordinary Levenshtein distance and at $m = 1$ a whole chunk acts like a single edit. On 67 Cluster G1 mycobacteriophage genomes (a viral group with MPME1 and MPME2), MPME1 targeting yielded $\sim 53 %$ discount for the 31-genome MPME1-score group and $\sim 9 %$ for the 11-genome MPME2-score group. MPME2 targeting reversed this pattern, with 18 phages low on both scores. For PV92, a 346-bp Yb8-containing insertion received 99.71% forward reduction at $m = 1$ and none in reverse. Together, these results demonstrate that MosaicLev can quantify the contribution of known mobile elements to sequence differences across distinct genomic settings.