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January 01, 2023 article Open access Aachen paper

A Boolean algebra for genetic variants

Bioinformatics, vol. 39

DOI: 10.1093/bioinformatics/btad001 Full text (OA) OpenAlex

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/mutalyzer/algebra/tree/v0.2.0 as well as an interface at https://mutalyzer.nl/algebra.

Authors 4

  1. Jonathan K. Vis corresponding Aachen Department of Human Genetics Leiden Institute of Advanced Computer Science

    Leiden University · Leiden University Medical Center

    Affiliation as printed

    Department of Human Genetics, Leiden University Medical Center , 2333 ZC Leiden, The Netherlands

    Leiden Institute of Advanced Computer Science, Leiden University , 2333 CA Leiden, The Netherlands

  2. Mark A Santcroos Aachen Department of Clinical Genetics Department of Human Genetics

    Leiden University Medical Center

    Affiliation as printed

    Department of Clinical Genetics, Leiden University Medical Center , 2333 ZC Leiden, The Netherlands

    Department of Human Genetics, Leiden University Medical Center , 2333 ZC Leiden, The Netherlands

  3. Walter A. Kosters Aachen Leiden Institute of Advanced Computer Science

    Leiden University

    Affiliation as printed

    Leiden Institute of Advanced Computer Science, Leiden University , 2333 CA Leiden, The Netherlands

  4. Jeroen F. J. Laros Aachen Department of Human Genetics

    Leiden University Medical Center · National Institute for Public Health and the Environment

    Affiliation as printed

    Department of Human Genetics, Leiden University Medical Center , 2333 ZC Leiden, The Netherlands

    National Institute for Public Health and the Environment (RIVM) , 3721 MA Bilthoven, The Netherlands

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References 31