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A Boolean algebra for genetic variants

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...

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Detalles Bibliográficos
Autores principales: Vis, Jonathan K, Santcroos, Mark A, Kosters, Walter A, Laros, Jeroen F J
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9879725/
https://www.ncbi.nlm.nih.gov/pubmed/36594541
http://dx.doi.org/10.1093/bioinformatics/btad001
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author Vis, Jonathan K
Santcroos, Mark A
Kosters, Walter A
Laros, Jeroen F J
author_facet Vis, Jonathan K
Santcroos, Mark A
Kosters, Walter A
Laros, Jeroen F J
author_sort Vis, Jonathan K
collection PubMed
description 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.
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spelling pubmed-98797252023-01-31 A Boolean algebra for genetic variants Vis, Jonathan K Santcroos, Mark A Kosters, Walter A Laros, Jeroen F J Bioinformatics Original Paper 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 2023-01-03 /pmc/articles/PMC9879725/ /pubmed/36594541 http://dx.doi.org/10.1093/bioinformatics/btad001 Text en © The Author(s) 2023. Published by Oxford University Press. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Original Paper
Vis, Jonathan K
Santcroos, Mark A
Kosters, Walter A
Laros, Jeroen F J
A Boolean algebra for genetic variants
title A Boolean algebra for genetic variants
title_full A Boolean algebra for genetic variants
title_fullStr A Boolean algebra for genetic variants
title_full_unstemmed A Boolean algebra for genetic variants
title_short A Boolean algebra for genetic variants
title_sort boolean algebra for genetic variants
topic Original Paper
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9879725/
https://www.ncbi.nlm.nih.gov/pubmed/36594541
http://dx.doi.org/10.1093/bioinformatics/btad001
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