Interpreting Sequence-Levenshtein distance for determining error type and frequency between two embedded sequences of equal length

TL;DR

This paper introduces a modified sequence-Levenshtein distance method that accurately distinguishes between frameshift errors and weighted errors in embedded biological sequences, improving error analysis in sequencing data.

Contribution

It proposes a novel modification to existing distance metrics, enabling better error type differentiation and weighting in biological sequence analysis.

Findings

Enhanced ability to distinguish frameshift errors from true errors

Accurate weighting of error types based on frequency

Improved error analysis in sequencing data

Abstract

Levenshtein distance is a commonly used edit distance metric, typically applied in language processing, and to a lesser extent, in molecular biology analysis. Biological nucleic acid sequences are often embedded in longer sequences and are subject to insertion and deletion errors that introduce frameshift during sequencing. These frameshift errors are due to string context and should not be counted as true biological errors. Sequence-Levenshtein distance is a modification to Levenshtein distance that is permissive of frameshift error without additional penalty. However, in a biological context Levenshtein distance needs to accommodate both frameshift and weighted errors, which Sequence-Levenshtein distance cannot do. Errors are weighted when they are associated with a numerical cost that corresponds to their frequency of appearance. Here, we describe a modification that allows the use of Levenshtein distance and Sequence-Levenshtein distance to appropriately accommodate penalty-free frameshift between embedded sequences and correctly weight specific error types.