A Boolean algebra for genetic variants

Vis, J.K.; Santcroos, M.A.; Kosters, W.A.; Laros, J.F.J. (2023)

Article / Letter to editor

MotivationBeyond 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.ResultsWe 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 implementationA Python implementation is available at as well as an interface at .

• All authors: Vis, J.K.; Santcroos, M.A.; Kosters, W.A.; Laros, J.F.J.
• Date: 2023-01-01
• Journal: Bioinformatics
• Volume: 39
• Issue: 1
• DOI: doi:10.1093/bioinformatics/btad001