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Rapid annotation method and device for a bacterial DNA sequence

A DNA sequence and bacteria technology, applied in sequence analysis, instrumentation, genomics, etc., can solve the problems of scattered, cumbersome, and a large number of manual operations in the analysis system, and achieve the effect of simplifying and optimizing the analysis process.

Pending Publication Date: 2020-12-01
ZHEJIANG UNIV +1
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Problems solved by technology

[0005] The purpose of the embodiments of the present invention is to provide a method and device for rapid annotation of bacterial DNA sequences to solve the problem that existing drug-resistant genes and mobile element analysis systems are scattered, annotations require a lot of manual operations and are extremely cumbersome, and the annotation speed is slow. Issues such as a stand-alone annotation system

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  • Rapid annotation method and device for a bacterial DNA sequence
  • Rapid annotation method and device for a bacterial DNA sequence
  • Rapid annotation method and device for a bacterial DNA sequence

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Embodiment 2

[0092] refer to Figure 4 , is a block diagram of a bacterial DNA sequence rapid annotation device provided in an embodiment of the present invention, the device can execute any of the bacterial DNA sequence rapid annotation methods provided in any embodiment of the present invention, and has corresponding functional modules for executing the method and beneficial effects. The unit includes:

[0093] Database construction module 901, for respectively constructing ResDB, ISDB, IntegronDB and TransposonDB database;

[0094] Obtaining module 902, for obtaining the bacterial DNA sequence to be analyzed;

[0095] Comparison module 903, for utilizing the BLASTN program to compare the bacterial DNA sequence to be analyzed with one or more of ResDB, ISDB, IntegronDB and TransposonDB databases;

[0096] The output module 904 is configured to obtain the sequence information of the aligned fragments of the best matching gene and the query gene corresponding to the best matching gene a...

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Abstract

The invention discloses a rapid annotation method and device for a bacterial DNA sequence. The method comprises the following steps: respectively constructing a ResDB database, an ISDB database, an IntegronDB database and a TranssposonDB database; obtaining a bacteria DNA sequence to be analyzed; comparing the bacteria DNA sequence to be analyzed with one or more of a ResDB database, an ISDB database, an IntegronDB database and a TranssposonDB database by using a BLASTN program; and according to the coverage rate and consistency of comparison, obtaining comparison fragment sequence informationof the optimal matching gene and the query gene corresponding to the optimal matching gene, and outputting an annotation result. The method is helpful for simplifying and optimizing the current genome analysis process and accelerating the subsequent genome analysis.

Description

technical field [0001] The invention relates to the field of bacterial DNA sequence annotation, in particular to a rapid bacterial DNA sequence annotation method and device, which are mainly used in the analysis of drug-resistant genomes, insertion elements, integrons and transposons of DNA series. Background technique [0002] In recent years, high-throughput genome sequencing (NGS) technology has achieved rapid development, which has greatly reduced the cost of sequencing bacterial genomes and increased the possibility of rapid bacterial genome-wide sequencing in clinical microbiology laboratories. One of the greatest advantages of NGS is the ability to predict drug resistance genes and mobile elements in a variety of bacteria, which accelerates the research process in the field of bacterial molecular characteristics and epidemiological surveillance. In a short period of time, a large number of bacterial genomes have been sequenced, and the number of genomes released has i...

Claims

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Application Information

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IPC IPC(8): G16B20/30G16B30/00
CPCG16B20/30G16B30/00
Inventor 华孝挺俞云松陈欢梁倩洪文杰何锦涛张玲虹
Owner ZHEJIANG UNIV
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