In:
Bioinformatics, Oxford University Press (OUP), Vol. 39, No. 1 ( 2023-01-01)
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. 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.
Type of Medium:
Online Resource
ISSN:
1367-4803
,
1367-4811
DOI:
10.1093/bioinformatics/btad001
Language:
English
Publisher:
Oxford University Press (OUP)
Publication Date:
2023
detail.hit.zdb_id:
1468345-3
SSG:
12
