A Boolean algebra for genetic variants
JK Vis, MA Santcroos, WA Kosters, JFJ Laros - Bioinformatics, 2023 - academic.oup.com
JK Vis, MA Santcroos, WA Kosters, JFJ Laros
Bioinformatics, 2023•academic.oup.comMotivation 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 …
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 …
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/mutalyzer/algebra/tree/v0.2.0 as well as an interface at https://mutalyzer.nl/algebra.
Oxford University Press