Inter-chromosomal k-mer distances.

ABSTRACT:

Background

Inversion Symmetry is a generalization of the second Chargaff rule, stating that the count of a string of k nucleotides on a single chromosomal strand equals the count of its inverse (reverse-complement) k-mer. It holds for many species, both eukaryotes and prokaryotes, for ranges of k which may vary from 7 to 10 as chromosomal lengths vary from 2Mbp to 200 Mbp. Building on this formalism we introduce the concept of k-mer distances between chromosomes. We formulate two k-mer distance measures, D₁ and D₂, which depend on k. D₁ takes into account all k-mers (for a single k) appearing on single strands of the two compared chromosomes, whereas D₂ takes into account both strands of each chromosome. Both measures reflect dissimilarit

SUBMITTER: Kafri A 

PROVIDER: S-EPMC8422766 | biostudies-literature | 2021 Sep

REPOSITORIES: biostudies-literature