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

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   ∈   [ 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 ∼ 53 % discount for the 31-genome MPME1-score group and ∼ 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. AVAILABILITY AND IMPLEMENTATION: Python implementation with Numba JIT compilation freely available at https://doi.org/10.5281/zenodo.18452982.