An efficient algorithm for the extraction of HGVS variant descriptions from sequences | Zendy

Jonathan K. Vis | Zendy; Martijn Vermaat | Zendy; Peter E.M. Taschner | Zendy; Joost N. Kok | Zendy; Jeroen F. J. Laros | Zendy

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An efficient algorithm for the extraction of HGVS variant descriptions from sequences

Author(s) -

Jonathan K. Vis,

Martijn Vermaat,

Peter E.M. Taschner,

Joost N. Kok,

Jeroen F. J. Laros

Publication year - 2015

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btv443

Subject(s) - python (programming language) , computer science , computation , algorithm , sequence (biology) , source code , extractor , programming language , biology , genetics , process engineering , engineering

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.

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