dbAPIS:对抗核细胞免疫系统基因的数据库
Yuchen Yan1, Jinfang Zheng2, Xinpeng Zhang1
1Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska - Lincoln, Lincoln, NE 68588, USA.
dbAPIS 是一种针对抗核细胞免疫系统 (APIS) 基因的新数据库,提供经过实验验证的数据和同质性搜索. 本资源有助于在菌体和其他移动遗传元素中发现新型抗防御基因.
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:
- 抗核细胞免疫系统 (APIS) 蛋白质由菌体,菌体和质粒编码,抵消细菌的防御机制,如限制修饰和CRISPR-Cas系统.
- 关于APIS基因的现有知识分散在文献中,阻碍了系统的研究和发现.
研究的目的:
- 开发dbAPIS,这是第一个对实验验证APIS基因及其蛋白质家族的数据库.
- 为研究 prokaryotic 免疫和菌-细菌相互作用的研究人员提供全面的资源.
主要方法:
- 文献策划以识别和收集实验验证APIS基因的数据.
- 开发一个包含蛋白质序列,功能注释,结构预测,基因组语境和同质性搜索的数据库.
- 将APIS蛋白质分类为基于序列的家族,并构建隐藏的马尔科夫模型 (HMM).
主要成果:
- 该dbAPIS数据库包括41个经过验证的APIS蛋白质和大约4400个序列对应物,跨越92个家族和38个氏族.
- 该库提供经过实验验证的APIS基因,蛋白质序列,功能注释,预测结构和基因组背景.
- 一个用户友好的网页界面允许浏览,搜索和下载APIS数据,包括对微生物组/病毒组数据库进行同类搜索.
结论:
- dbAPIS 作为一个有价值的,集中资源,用于研究APIS蛋白质,促进新型抗防御基因的发现.
- 该数据库支持研究 prokaryotic 防御系统及其抑制剂的演变和功能.
- dbAPIS通过同源性搜索和数据可访问性,增强了对菌体的抗防御基因和基因组岛屿的发现.
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