MosaicLev: Modified Levenshtein distance for mobile element-aware genome comparison

Motivation Somatic genetic mosaicism arises when genomes diverge across cells during development, in part due to the activity of transposons (cut–paste) and retrotransposons (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.

We introduce a modified Levenshtein distance (mlev) that discounts mobile element insertions via a tunable parameter (m ∈ [0, 1]). Validation on 67 Cluster G1 mycobacteriophage genomes demonstrates bidirectional discrimination between Mycobacteriophage Mobile Element 1 (MPME1) and MPME2 elements: using MPME1 as target yields ∼49% discount for MPME1 carriers but only ∼9% for MPME2 carriers, while using MPME2 reverses this pattern. This approach classifies 35 MPME1 carriers and 11 MPME2 carriers, and identifies 14 phages showing low discount with both motifs, consistent with absence of both elements. Availability and Implementation Python implementation with Numba JIT compilation freely available at https://doi.org/10.5281/zenodo.18452982. Competing Interest Statement The authors have declared no competing interest. Footnotes Contact thomas.kuhlman{at}ucr.edu Supplementary information Supplementary data, analysis scripts, and pairwise distance matrices are available at the GitHub repository. Abbreviations - MPME - Mycobacteriophage Mobile Element - mlev - modified Levenshtein distance - DP - dynamic programming