使用 BioAtlas 进行交互式微生物分布分析。
Interactive microbial distribution analysis using BioAtlas.
机构信息
Department of Mathematics and Computer Science (IMADA), University of Southern Denmark, 5000 Odense, Denmark.
Max Planck Institute for Informatics, Saarland Informatics Campus, 66123 Saarbrücken, Germany.
出版信息
Nucleic Acids Res. 2017 Jul 3;45(W1):W509-W513. doi: 10.1093/nar/gkx304.
UNLABELLED
Massive amounts of 16S rRNA sequencing data have been stored in publicly accessible databases, such as GOLD, SILVA, GreenGenes (GG), and the Ribosomal Database Project (RDP). Many of these sequences are tagged with geo-locations. Nevertheless, researchers currently lack a user-friendly tool to analyze microbial distribution in a location-specific context. BioAtlas is an interactive web application that closes this gap between sequence databases, taxonomy profiling and geo/body-location information. It enables users to browse taxonomically annotated sequences across (i) the world map, (ii) human body maps and (iii) user-defined maps. It further allows for (iv) uploading of own sample data, which can be placed on existing maps to (v) browse the distribution of the associated taxonomies. Finally, BioAtlas enables users to (vi) contribute custom maps (e.g. for plants or animals) and to map taxonomies to pre-defined map locations. In summary, BioAtlas facilitates map-supported browsing of public 16S rRNA sequence data and analyses of user-provided sequences without requiring manual mapping to taxonomies and existing databases.
AVAILABILITY
未标记
大量的 16S rRNA 测序数据已存储在公共可访问的数据库中，例如 GOLD、SILVA、GreenGenes（GG）和核糖体数据库项目（RDP）。这些序列中的许多都带有地理位置标签。然而，研究人员目前缺乏一种用户友好的工具来分析特定位置的微生物分布。BioAtlas 是一个交互式网络应用程序，它填补了序列数据库、分类分析和地理/身体位置信息之间的空白。它使用户能够在（i）世界地图、（ii）人体地图和（iii）用户定义的地图上浏览分类注释的序列。它进一步允许（iv）上传自己的样本数据，这些数据可以放置在现有地图上，以（v）浏览相关分类的分布。最后，BioAtlas 使用户能够（vi）贡献自定义地图（例如用于植物或动物），并将分类映射到预定义的地图位置。总之，BioAtlas 便于在支持地图的环境中浏览公共 16S rRNA 序列数据，并分析用户提供的序列，而无需手动将其映射到分类和现有数据库。
可用性
Zotero 插件