Method for constructing antibiotic resistance genbank

A technology of antibiotic resistance and resistance genes, applied in the field of bioinformatics, can solve problems such as sequence deviation

Active Publication Date: 2018-09-04
RES CENT FOR ECO ENVIRONMENTAL SCI THE CHINESE ACAD OF SCI +1
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Problems solved by technology

[0004] Aiming at the sequence deviation problem that may be caused in the process of constructing the current antibiotic resistance gene database, the present invention proposes for the first time that according to the hidden Markov model, the key conserved sites of the protein sequence are identified, and the key points of the gene protein sequence are searched, screened and determined. technology, the main purpose of which is to provide a construction method for constructing an antibiotic resistance gene database

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  • Method for constructing antibiotic resistance genbank
  • Method for constructing antibiotic resistance genbank
  • Method for constructing antibiotic resistance genbank

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[0025] In order to make the object, technical solution and advantages of the present invention clearer, the present invention will be further described in detail below in conjunction with specific examples.

[0026] The present invention will be further described below, taking the polymyxin resistance gene MCR-1 as an example.

[0027] (1) Search the polymyxin resistance gene MCR-1 in the gene database (GenBank) (https: / / www.ncbi.nlm.nih.gov / ), and obtain the protein sequence corresponding to MCR-1:

[0028]

[0029] (2) According to the reference (Liu, Y.Y., Wang Y., Walsh T.W., et al. 2016.ARDB-Antibiotic Resistance Genes Database. Nucleic Acids Research 37, D443-D447), the length of the target fragment of the MCR-1 gene is determined to be about About 541bp, set the sequence length range between 491bp-591bp, and the sequence annotation information should include the name of the MCR-1 gene, download the sequence that meets the requirements, delete the repeated sequence an...

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Abstract

The invention discloses a bioinformatics method for constructing an antibiotic resistance genbank in the biotechnology field. The method comprises the following steps that: searching the protein sequence of a resistance gene in a GenBank; selecting a sequence with high accuracy as an initial sequence; adopting a Clustalw method for comparison; constructing a hidden Markov model, and searching a GenBank protein database to obtain all sequences which contain protein conserved sites; according to the E values of the sequences and the annotation information of the sequences in the GenBank database, removing the sequences which are highly homologous and do not conform to requirements; and after repeated sequences are removed, adding species annotation information; and integrating all protein sequences to finish database construction. By use of the method, the annotation information and the comparison similarity of a sequence can be comprehensively measured, and sequence collection speed andaccuracy can be improved. By use of the method provided by the invention, the construction of the antibiotic resistance genbank can be finished, and a basic data is provided for researching the primer design, the data analysis and the sequence annotation of the resistance gene.

Description

technical field [0001] The invention relates to the field of biotechnology, in particular to a bioinformatics method for establishing an antibiotic resistance gene database based on a hidden Markov model of protein conservative sites. Background technique [0002] The current method of constructing an antibiotic resistance gene database is mainly to directly search and extract the resistance gene sequence from the GenBank database according to the name of the resistance gene or other relevant information, and then perform deletion and filtering, such as the antibiotic resistance gene database ARDB (Antibiotic Resistance Database: Liu, B. and Pop, M.2009.ARDB-Antibiotic Resistance Genes Database. Nucleic Acids Research 37, D443-D447) and CARD (Comprehensive Antibiotic Resistance Database: Yan, M., Yu, T. and Wright, G.D.2013. The Comprehensive Antibiotic Resistance Database.AntimicrobialAgents and Chemotherapy 57(7), 3348-3357) etc.; but this method relies on the annotation i...

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G06F19/28
CPCG16B50/00Y02A90/10
Inventor 邓晔魏子艳
Owner RES CENT FOR ECO ENVIRONMENTAL SCI THE CHINESE ACAD OF SCI
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