Abstract
The article discusses the possible “physical” meaning of the distance between genetic sequences, based on comparing the set of all words of fixed length (N-gram) occurring in two genomic sequences. The considered distances suitable describe phylogenetic relationships and allow ranking by the genomes similarities in situations where it is practically impossible to provide by alignment methods. A simulation shows that the distances between the N-gram distributions change almost linearly, with genome lengths growing for relatively small artificial evolutionary modifications. In the general case of comparing two genetic texts, a function for “calibrating” the distance between N-gram distributions is found. This fact makes it possible to interpret the considered distances by means of the number of elementary operators performed in an alignment process between the compared sequences.
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Kirzhner, V., Volkovich, Z. Application of N-Gram Based Distances to Genetic Texts Comparison. Biosemiotics 14, 271–285 (2021). https://doi.org/10.1007/s12304-021-09442-y
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DOI: https://doi.org/10.1007/s12304-021-09442-y