Title:
METHOD FOR DETECTING RECOMBINATION BETWEEN SARS-COV-2 LINEAGES ON THE BASIS OF INFORMATION THEORY
Document Type and Number:
WIPO Patent Application WO/2023/240947
Kind Code:
A1
Abstract:
Provided in the present invention is a method for detecting the recombination between SARS-CoV-2 lineages on the basis of information theory, comprising: constructing a consensus sequence from lineage sequences to be queried, and marking the base with the largest content at each site and the corresponding proportion; merging the queried lineage sequences with other reference lineage sequences, and then performing multiple sequence alignment to obtain an alignment sequence file; selecting whether to retain gap sites in the alignment sequence file or not, and extracting polymorphic sites; calculating the recombination contribution value provided by each reference lineage sequence for the queried lineage sequences at each polymorphic site; calculating the average recombination contribution value provided by each reference lineage sequence at the sites in the sliding window, and detecting recombination fragments from potential parents; splicing the contiguous and non-contiguous recombinant fragments on the potential parents into recombinant regions, and determining whether the recombinant regions are false positive or not; and with reference to the polymorphic sites and recombination contribution values in the reference lineage sequences, searching potential recombination breakpoints at the boundaries of recombinant regions.
Inventors:
GE XINGYI (CN)
ZHOU ZHIJIAN (CN)
YE SHENGBAO (CN)
QIU YE (CN)
ZHOU ZHIJIAN (CN)
YE SHENGBAO (CN)
QIU YE (CN)
Application Number:
PCT/CN2022/137508
Publication Date:
December 21, 2023
Filing Date:
December 08, 2022
Export Citation:
Assignee:
UNIV HUNAN (CN)
International Classes:
G16B30/10; G16B20/30; G16B30/20
Foreign References:
| CN114743598A | 2022-07-12 | |||
| CN111004869A | 2020-04-14 | |||
| CN102367490A | 2012-03-07 | |||
| CN107889508A | 2018-04-06 |
Other References:
QIN ZUODONG, MAO QIANZHUO, DING AIPING, JIN LEILEI, PENG WENJUN, DU ZHIYOU, SHENTU SUSU, CHEN JISHUANG: "Sequence Characterization and Molecular Detection of the 3'-Terminal Region of Bean Yellow Mosaic Virus Infecting Canna", 2010 4TH INTERNATIONAL CONFERENCE ON BIOINFORMATICS AND BIOMEDICAL ENGINEERING, IEEE, 1 June 2010 (2010-06-01) - 20 June 2010 (2010-06-20), pages 1 - 4, XP093117899, ISSN: 2151-7614, ISBN: 978-1-4244-4713-8, DOI: 10.1109/ICBBE.2010.5515708
Attorney, Agent or Firm:
SHENZHEN SHUN LI INTELLECTUAL PROPERTY FIRM (CN)
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