A Boolean algebra for genetic variants.
basic_science · Level V
Where this comes from
- Record sourced from PubMed, PMID 36594541.
- Also identified by DOI 10.1093/bioinformatics/btad001 and PMC identifier 9879725.
- Licence recorded as CC BY.
- The licence permits redistribution, so the abstract is shown in full and the full text is available from the publisher.
Abstract
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. 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. A Python implementation is available at https://github.com/mutalyzer/algebra/tree/v0.2.0 as well as an interface at https://mutalyzer.nl/algebra.
Medical subject headings
- Algorithms
- Data Management