varDB: a pathogen-specific sequence database of protein families involved in antigenic variation
varDB: a pathogen-specific sequence database of protein families involved in antigenic variation
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DOI：
10.1093/bioinformatics/btn477
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发表时间：
2008-11-01
期刊：
影响因子：
5.8
通讯作者：
Goto, Susumu
中科院分区：
文献类型：
--
作者：
Hayes, C. Nelson;Diez, Diego;Goto, Susumu
传染病是全球公共卫生和繁荣的主要威胁。病原体包括一系列病原体，从细菌到病毒，包括真菌、蠕虫和原生动物。虽然这些生物体的生物结构和与宿主的相互作用极其不同，但它们逃避宿主免疫系统的方法相似。抗原变异和漂移是病原体改变其暴露的表位同时维持蛋白质功能的机制。因此，这些特征使病原体能够在宿主中建立慢性感染。开发varDB数据库是为了作为蛋白质和核苷酸序列以及相关特征（例如，田间分离株数据、临床参数等）的中央储存库。与抗原变异有关。目前varDB中包含的数据是从GenBank以及多个专门的数据存储库（例如PlasmoDB，GiardiaDB）中挖掘出来的。使用分层检索策略（包括基于文献/作者的检索和HMM特征）确定家族成员和直系同源物组。目前的版本包括来自25种不同病原体的39个基因家族的29000个序列。这一资源将使研究人员能够比较分类群内和分类群间的抗原变异，目的是确定致病性的共同机制，以协助对抗一系列毁灭性疾病。
Infectious diseases are a major threat to global public health and prosperity. The causative agents consist of a suite of pathogens, ranging from bacteria to viruses, including fungi, helminthes and protozoa. Although these organisms are extremely varied in their biological structure and interactions with the host, they share similar methods of evading the host immune system. Antigenic variation and drift are mechanisms by which pathogens change their exposed epitopes while maintaining protein function. Accordingly, these traits enable pathogens to establish chronic infections in the host. The varDB database was developed to serve as a central repository of protein and nucleotide sequences as well as associated features (e.g. field isolate data, clinical parameters, etc.) involved in antigenic variation. The data currently contained in varDB were mined from GenBank as well as multiple specialized data repositories (e.g. PlasmoDB, GiardiaDB). Family members and ortholog groups were identified using a hierarchical search strategy, including literature/author-based searches and HMM profiles. Included in the current release are29 000 sequences from 39 gene families from 25 different pathogens. This resource will enable researchers to compare antigenic variation within and across taxa with the goal of identifying common mechanisms of pathogenicity to assist in the fight against a range of devastating diseases.