Estimation of substitution and indel rates via <i>k</i>-mer statistics.

ABSTRACT: Methods utilizing k -mers are widely used in bioinformatics, yet our understanding of their statistical properties under realistic mutation models remains incomplete. Previously, substitution-only mutation models have been considered to derive precise expectations and variances for mutated k -mers and intervals of mutated and non-mutated sequences. In this work, we consider a mutation model that incorporates insertions and deletions in addition to single-nucleotide substitutions. Within this framework, we derive closed-form k -mer-based estimators for the three fundamental mutation parameters: substitution, deletion rate, and insertion rates. We provide theoretical guarantees in the form of concentration inequalities, ensuring accuracy of our estimators under reasonable model assumptions.

SUBMITTER: Hera MR 

PROVIDER: S-EPMC12132262 | biostudies-literature | 2025 Jul

REPOSITORIES: biostudies-literature