使用ATCCfinder来识别商业上可用的美国型文化收藏品菌株,基于序列查询
Samuel I Koehler1, Earl A Middlebrook1, Blake T Hovde1
1Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States of America.
PeerJ
|August 18, 2025
概括
研究人员现在可以使用ATCCfinder软件轻松找到商用微生物菌株和目标基因. 该工具有效地搜索美国类型文化收集 (ATCC) 数据库中的同源序列,简化菌株识别和微生物学研究中的验证.
科学领域:
- 微生物学 微生物学
- 生物信息学是一种生物信息学.
- 基因组学就是基因组学.
背景情况:
- 历史微生物学研究经常使用由于测序资源有限而难以识别或验证的菌株.
- 从序列数据中识别商业上可用的微生物菌株或特定基因是具有挑战性的,阻碍了研究可重复性和发现.
- 公共序列数据库包含可变质量的数据,因此很难可靠地将序列与特定的,高质量的参考菌株联系起来,例如来自美国类型文化收藏 (ATCC) 的基因.
研究的目的:
- 开发一个软件工具,ATCCfinder,用于在ATCC数据库中高效地搜索和识别商用微生物菌株和遗传组件.
- 克服现有方法的局限性,用于查询与精选的ATCC参考基因组相对应的序列相似性.
- 为了促进历史微生物菌株的验证和从元基因组学研究中发现具有所需遗传元素的菌株.
主要方法:
- ATCCfinder使用ATCC应用程序编程接口 (API) 来访问并从ATCC基因组资源中生成可查询的数据库,包括序列,元数据和注释数据.
- 核酸查询与ATCC参考基因组进行比较,使用minimap2序列对齐工具.
- 结果被解析和分析,以提供对ATCC可用的菌株同源序列匹配的摘要,并具有识别和下载新的ATCC引用的能力.
主要成果:
- ATCCfinder成功地从ATCC序列,元数据和注释数据生成可查询的数据库.
- 该软件有效地识别可购买的ATCC菌株,这些菌株与查询序列相同,包括历史隔离物,功能基因和操作子.
- 通过识别和下载新的ATCC引用,ATCCfinder提供了一个更新的目标搜索数据库.
结论:
- ATCCfinder为访问,查询和总结ATCC微生物资源提供了一种高效的解决方案.
- 该软件简化了商用菌株和遗传组件的识别,支持微生物学研究和菌株验证.
- ATCCfinder增强了将序列数据与ATCC提供的特定,高质量的微生物参考菌株相连接的能力.
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