Chair for Clinical Bioinformatics, Saarland University, Campus Building E2.1, 66123 Saarbruecken, Germany.
Nucleic Acids Res. 2019 Jan 8;47(D1):D195-D202. doi: 10.1093/nar/gky1050.
The study of bacterial isolates or communities requires the analysis of the therein included plasmids in order to provide an extensive characterization of the organisms. Plasmids harboring resistance and virulence factors are of especial interest as they contribute to the dissemination of antibiotic resistance. As the number of newly sequenced bacterial genomes is growing a comprehensive resource is required which will allow to browse and filter the available plasmids, and to perform sequence analyses. Here, we present PLSDB, a resource containing 13 789 plasmid records collected from the NCBI nucleotide database. The web server provides an interactive view of all obtained plasmids with additional meta information such as sequence characteristics, sample-related information and taxonomy. Moreover, nucleotide sequence data can be uploaded to search for short nucleotide sequences (e.g. specific genes) in the plasmids, to compare a given plasmid to the records in the collection or to determine whether a sample contains one or multiple of the known plasmids (containment analysis). The resource is freely accessible under https://ccb-microbe.cs.uni-saarland.de/plsdb/.
该研究的细菌分离株或社区需要分析其中包含的质粒,以提供对生物体的广泛描述。携带耐药性和毒力因子的质粒特别令人关注,因为它们有助于抗生素耐药性的传播。随着新测序的细菌基因组数量的增加,需要一个全面的资源,该资源将允许浏览和筛选可用的质粒,并进行序列分析。在这里,我们介绍 PLSDB,这是一个包含从 NCBI 核苷酸数据库收集的 13789 个质粒记录的资源。该网络服务器提供了所有获得的质粒的交互式视图,并提供了附加的元信息,如序列特征、样本相关信息和分类学。此外,可以上传核苷酸序列数据来搜索质粒中的短核苷酸序列(例如特定基因),将给定的质粒与集合中的记录进行比较,或者确定样本是否包含一个或多个已知质粒(包含分析)。该资源可在 https://ccb-microbe.cs.uni-saarland.de/plsdb/ 下免费访问。