K-nonical space: sketching with reverse complements.

ABSTRACT:

Motivation

Sequences equivalent to their reverse complements (i.e. double-stranded DNA) have no analogue in text analysis and non-biological string algorithms. Despite this striking difference, algorithms designed for computational biology (e.g. sketching algorithms) are designed and tested in the same way as classical string algorithms. Then, as a post-processing step, these algorithms are adapted to work with genomic sequences by folding a k-mer and its reverse complement into a single sequence: The canonical representation (k-nonical space).

Results

The effect of using the canonical representation with sketching methods is understudied and not understood. As a first step, we use context-free sketching methods to illustrate the potentially detrimental effects of using cano

SUBMITTER: Marcais G 

PROVIDER: S-EPMC11549021 | biostudies-literature | 2024 Nov

REPOSITORIES: biostudies-literature