Title:
QUERY SEQUENCE GENOTYPE OR SUBTYPE CLASSIFICATION METHOD
Document Type and Number:
WIPO Patent Application WO/2011/105667
Kind Code:
A1
Abstract:
The present invention relates to a query sequence genotype or subtype classification method. More particularly, the present invention relates to a query sequence genotype or subtype classification method comprising the steps of: (i) adopting the base sequences of multiple viruses for which the genotypes or subtypes are known as reference sequences, and calculating distances between the sequences in a multi-sort thereof to obtain a distance matrix; and (ii) clustering the reference sequences by means of the multidimensional scaling of the distance matrix to obtain clusters on which discriminant analysis is performed to derive a discriminant for classifying the reference sequences, and classifying query sequence genotypes or subtypes according to the discriminant.
Inventors:
KIM SANG-SOO (KR)
Application Number:
PCT/KR2010/005337
Publication Date:
September 01, 2011
Filing Date:
August 13, 2010
Export Citation:
Assignee:
FOUNDATION SOONGSIL UNIV INDUSTRY COOPERATION (KR)
KIM SANG-SOO (KR)
KIM SANG-SOO (KR)
International Classes:
C12Q1/68; G16B40/30; G06F17/10; G06F19/00; G16B30/10
Other References:
MYERS ET AL.: "A statistical model for HIV-1 sequence classification using the subtype analyzer (STAR)", BIOINFORMATICS, vol. 21, no. 17, 26 July 2005 (2005-07-26), pages 3535 - 3540
GIFFORD ET AL.: "UK Collaborative Group on HIV Drug Resistance: Assessment of automated genotyping protocols as tools for surveillance of HIV-1 genetic diversity", AIDS, vol. 20, no. 11, 13 July 2006 (2006-07-13), pages 1521 - 1529
WU ET AL.: "Nucleotide composition string selection in HIV-1 subtyping using whole genomes", BIOINFORMATICS, vol. 23, no. 14, 11 May 2007 (2007-05-11), pages 1744 - 1752
ZHANG ET AL.: "jpHMM at GOBICS: a web server to detect genomic recombinations in HIV-1", NUCLEIC ACIDS RESEARCH, vol. 34, 1 July 2006 (2006-07-01), pages W463 - W465
DE OLIVEIRA ET AL.: "An automated genotyping system for analysis of HIV-1 and other microbial sequences", BIOINFORMATICS, vol. 21, no. 19, 2 August 2005 (2005-08-02), pages 3797 - 3800
GIFFORD ET AL.: "UK Collaborative Group on HIV Drug Resistance: Assessment of automated genotyping protocols as tools for surveillance of HIV-1 genetic diversity", AIDS, vol. 20, no. 11, 13 July 2006 (2006-07-13), pages 1521 - 1529
WU ET AL.: "Nucleotide composition string selection in HIV-1 subtyping using whole genomes", BIOINFORMATICS, vol. 23, no. 14, 11 May 2007 (2007-05-11), pages 1744 - 1752
ZHANG ET AL.: "jpHMM at GOBICS: a web server to detect genomic recombinations in HIV-1", NUCLEIC ACIDS RESEARCH, vol. 34, 1 July 2006 (2006-07-01), pages W463 - W465
DE OLIVEIRA ET AL.: "An automated genotyping system for analysis of HIV-1 and other microbial sequences", BIOINFORMATICS, vol. 21, no. 19, 2 August 2005 (2005-08-02), pages 3797 - 3800
Attorney, Agent or Firm:
SEO, Keun Bok (KR)
서근복 (KR)
서근복 (KR)
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Claims:
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