A Boolean algebra for genetic variants.

ABSTRACT:

Motivation

Beyond identifying genetic variants, we introduce a set of Boolean relations, which allows for a comprehensive classification of the relations of every pair of variants by taking all minimal alignments into account. We present an efficient algorithm to compute these relations, including a novel way of efficiently computing all minimal alignments within the best theoretical complexity bounds.

Results

We show that these relations are common, and many non-trivial, for variants of the CFTR gene in dbSNP. Ultimately, we present an approach for the storing and indexing of variants in the context of a database that enables efficient querying for all these relations.

Availability and implementation

A Python implementation is available at https://github.com/mutalyze

SUBMITTER: Vis JK 

PROVIDER: S-EPMC9879725 | biostudies-literature | 2023 Jan

REPOSITORIES: biostudies-literature