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

Bioinformatics

Volumn 31, Issue 23, 2015, Pages 3751-3757

  Vis, Jonathan K ^a,b   Vermaat, Martijn ^a   Taschner, Peter E M ^a,c   Kok, Joost N ^a,b   Laros, Jeroen F J ^a  

^a LEIDEN UNIVERSITY MEDICAL CENTER   (Netherlands)

^b LEIDEN UNIVERSITY   (Netherlands)

^c UNIVERSITY OF APPLIED SCIENCES LEIDEN   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; DNA SEQUENCE; GENETIC VARIATION; HUMAN; HUMAN GENOME; PROCEDURES;

ALGORITHMS; GENETIC VARIATION; GENOME, HUMAN; HUMANS; SEQUENCE ANALYSIS, DNA;

EID: 84950237588     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btv443     Document Type: Article

References (12)

1. Abbasi, S. (1997) Longest common consecutive substring in two random strings. Technical report, Report number: 97-65. Center for Discrete Mathematics & Theoretical Computer Science.
2. Brandon, M.C. et al. (2009) Data structures and compression algorithms for genomic sequence data. Bioinformatics, 25, 1731-1738.
3. Compeau, P.E. et al. (2011) How to apply de Bruijn graphs to genome assembly. Nat. Biotechnol., 29, 987-991.
4. Den Dunnen, J.T. et al. (2000) Mutation nomenclature extensions and suggestions to describe complex mutations: a discussion. Hum. Mutat., 15, 7-12.
5. Gusfield, D. (1997) Algorithms on Strings, Trees and Sequences: Computer Science and Computational Biology. Cambridge University Press, Cambridge, United Kingdom.
6. Robinson, J. et al. (2015) The IPD and IMGT/HLA database: Allele variant databases. Nucleic Acids Res., 43, 23-431.
7. Smith, T.F. and Waterman, M.S. (1981) Identification of common molecular subsequences. J. Mol. Biol., 147, 195-197.
8. Taschner, P.E. and Den Dunnen, J.T. (2011) Describing structural changes by extending HGVS sequence variation nomenclature. Hum. Mutat., 32, 507-511.
9. Tichy, W.F. (1984) The string-to-string correction problem with block moves. TOCS, 2, 309-321.
10. Wagner, R.A. and Fischer, M.J. (1974) The string-to-string correction problem. JACM, 21, 168-173.
11. Wagner, R.A. and Lowrance, R. (1975) An extension of the string-to-string correction problem. JACM, 22, 177-183.
12. Wildeman, M. et al. (2008) Improving sequence variant descriptions in mutation databases and literature using the Mutalyzer sequence variation nomenclature checker. Hum. Mutat., 29, 6-13.