GAS-J,一个用于化脓性链球菌基因组组装、emm分型、MLST分型和毒力因子基因检测的用户友好浏览器应用程序。

IF 1.9 4区 医学 Q4 IMMUNOLOGY
Norihiko Takemoto, Kohei Ogura, Yuan Gao, Rumi Okuno, Masaya Yamaguchi, Yujiro Hirose, Masayuki Ono, Shigetada Kawabata, Tadayoshi Ikebe, Takashi Hamabata, Tohru Miyoshi-Akiyama
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引用次数: 0

摘要

临床分离的化脓性链球菌通常采用emm和多位点序列分型(MLST)进行分类。近年来,全基因组测序(WGS)已被用于emm分型和MLST分析。WGS数据提供了关于毒力因子基因存在的额外信息。为了使不熟悉生物信息学的研究人员能够分析化脓链球菌的WGS数据,我们开放了一个名为GAS-J的在线工具,该工具可以自动输出emm类型、序列类型(STs)、毒力因子基因携带和系统发育树。该工具接受原始的短读数据作为输入,因为它包含了天鹅绒汇编程序。在所有分离株中,该工具的emm分型结果与传统PCR和Sanger测序获得的结果相同,即使在分离株具有伪emm (emm样)基因的情况下也是如此。STs是通过使用7个等位基因作为参考执行BLAST搜索来确定的。为了检测化脓链球菌毒力因子基因,我们准备了一个包含620个相关蛋白的新数据集。用户可以从406株具有流行病学数据的分离株中选择将哪些分离株纳入基于snp的系统发育树。该数据集包括根据《日本传染病防治法》的STSS标准诊断出症状(STSS或非STSS)的分离株。GAS-J应用程序可从http://gasj.ncgm.go.jp获得。分离株的数据将在未来进行更新。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
GAS-J, a User-Friendly Browser Application for Genome Assembly, emm-Typing, MLST Typing, and Virulence Factor Gene Detection of Streptococcus pyogenes.

Clinical isolates of Streptococcus pyogenes are usually classified using emm and multilocus sequence typing (MLST). Recently, whole genome sequencing (WGS) has been employed for emm typing and MLST analysis. WGS data provides additional information on the presence of virulence factor genes. To enable researchers unfamiliar with bioinformatics to analyze WGS data of S. pyogenes, we opened an online tool named GAS-J, which automatically outputs emm types, sequence types (STs), carriage of virulence factor genes, and phylogenetic trees. The tool accepts raw short-read data as inputs, since it includes the velvet assembler. In all isolates, the emm typing results from this tool were identical to those obtained by conventional PCR and Sanger sequencing, even in cases where isolates had pseudo-emm (emm-like) genes. STs are determined by performing a BLAST search using seven alleles as references. To detect S. pyogenes virulence factor genes, we prepared a new data set containing 620 related proteins. Users may choose which isolates to include in SNP-based phylogenetic tree from a pool of 406 isolates with epidemiological data. The data set includes isolates whose symptoms (STSS or non-STSS) were diagnosed based on the STSS criteria of the Japan Communicable Disease Prevention Law. GAS-J application is available at http://gasj.ncgm.go.jp. The data of isolates are going to be updated in the future.

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来源期刊
Microbiology and Immunology
Microbiology and Immunology 医学-免疫学
CiteScore
5.20
自引率
3.80%
发文量
78
审稿时长
1 months
期刊介绍: Microbiology and Immunology is published in association with Japanese Society for Bacteriology, Japanese Society for Virology, and Japanese Society for Host Defense Research. It is peer-reviewed publication that provides insight into the study of microbes and the host immune, biological and physiological responses. Fields covered by Microbiology and Immunology include:Bacteriology|Virology|Immunology|pathogenic infections in human, animals and plants|pathogenicity and virulence factors such as microbial toxins and cell-surface components|factors involved in host defense, inflammation, development of vaccines|antimicrobial agents and drug resistance of microbes|genomics and proteomics.
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