An efficient algorithm for the extraction of HGVS variant descriptions from sequences.
Bioinformatics
; 31(23): 3751-7, 2015 Dec 01.
Article
em En
| MEDLINE
| ID: mdl-26231427
ABSTRACT
MOTIVATION Unambiguous sequence variant descriptions are important in reporting the outcome of clinical diagnostic DNA tests. The standard nomenclature of the Human Genome Variation Society (HGVS) describes the observed variant sequence relative to a given reference sequence. We propose an efficient algorithm for the extraction of HGVS descriptions from two sequences with three main requirements in mind minimizing the length of the resulting descriptions, minimizing the computation time and keeping the unambiguous descriptions biologically meaningful. RESULTS:
Our algorithm is able to compute the HGVS descriptions of complete chromosomes or other large DNA strings in a reasonable amount of computation time and its resulting descriptions are relatively small. Additional applications include updating of gene variant database contents and reference sequence liftovers.AVAILABILITY:
The algorithm is accessible as an experimental service in the Mutalyzer program suite (https//mutalyzer.nl). The C++ source code and Python interface are accessible at https//github.com/mutalyzer/description-extractor. CONTACT j.k.vis@lumc.nl.
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Base de dados:
MEDLINE
Assunto principal:
Variação Genética
/
Algoritmos
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Análise de Sequência de DNA
Idioma:
En
Ano de publicação:
2015
Tipo de documento:
Article