title: An efficient algorithm for the extraction of HGVS variant descriptions from sequences.
abstract: BACKGROUND
  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.
  
  
  BACKGROUND
  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.
  
  
  BACKGROUND
  j.k.vis@lumc.nl.
authors.affiliation: Department of Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands, Leiden Institute of Advanced Computer Science, Leiden University, Leiden, The Netherlands.
authors.forename: Jonathan K
authors.initials: JK
authors.lastname: Vis
authors.affiliation: Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands.
authors.forename: Martijn
authors.initials: M
authors.lastname: Vermaat
authors.affiliation: Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands, Generade Center of Expertise Genomics, University of Applied Sciences Leiden, Leiden, The Netherlands and.
authors.forename: Peter E M
authors.initials: PE
authors.lastname: Taschner
authors.affiliation: Department of Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands, Leiden Institute of Advanced Computer Science, Leiden University, Leiden, The Netherlands.
authors.forename: Joost N
authors.initials: JN
authors.lastname: Kok
authors.affiliation: Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands, Leiden Genome Technology Center, Leiden University Medical Center, Leiden, The Netherlands.
authors.forename: Jeroen F J
authors.initials: JF
authors.lastname: Laros
mesh_terms: D000465:Algorithms; D014644:Genetic Variation; D015894:Genome, Human; D006801:Humans; D017422:Sequence Analysis, DNA / Q000379:methods*