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Levenshtein distance is a commonly used edit distance metric, typicallyapplied in language processing, and to a lesser extent, in molecular biologyanalysis. Biological nucleic acid sequences are often embedded in longersequences and are subject to insertion and deletion errors that introduceframeshift during sequencing. These frameshift errors are due to string contextand should not be counted as true biological errors. Sequence-Levenshteindistance is a modification to Levenshtein distance that is permissive offrameshift error without additional penalty. However, in a biological contextLevenshtein distance needs to accommodate both frameshift and weighted errors,which Sequence-Levenshtein distance cannot do. Errors are weighted when theyare associated with a numerical cost that corresponds to their frequency ofappearance. Here, we describe a modification that allows the use of Levenshteindistance and Sequence-Levenshtein distance to appropriately accommodatepenalty-free frameshift between embedded sequences and correctly weightspecific error types.

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