Seqenv: linking sequences to environments through text mining.
Seqenv: linking sequences to environments through text mining.
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作者：
Sinclair L;Ijaz UZ;Jensen LJ;Coolen MJL;Gubry-Rangin C;Chroňáková A;Oulas A;Pavloudi C;Schnetzer J;Weimann A;Ijaz A;Eiler A;Quince C;Pafilis E
了解不同环境中类群和相关性状的分布是微生物生态学的核心问题之一。高通量测序（HTS）研究目前正在产生大量的数据，以解决这一地理主题。然而，这些研究通常集中在特定的环境类型或过程上，导致产生单独的、不相连的数据集。可以利用现有的大量遗留序列数据和相关元数据，更好地将这些调查中发现的遗传信息置于更广泛的环境背景中。在这里，我们介绍一个软件程序，seqenv，来执行这样的任务。它自动执行短序列的相似性搜索，对NCBI提供的“nt”核苷酸数据库，并在每次命中，提取-如果它是可用的-文本元数据字段。在从所有搜索结果中收集所有隔离源之后，我们运行文本挖掘算法来识别和解析与环境本体（EnvO）控制词汇表相关联的单词。这反过来又使我们能够确定在哪些环境中以前观察到单个序列或分类群，并通过这些结果的加权求和来总结完整的样本。我们提出了两个示范应用seqenv氨氧化古菌的调查，以及从黑海的浮游生物古生物数据集。这些都证明了该工具的能力，揭示新的模式，在高温超导及其实用程序的环境源跟踪，古生物学和微生物群落学的研究领域。要安装seqenv，请访问：https://github.com/xapple/seqenv。
Understanding the distribution of taxa and associated traits across different environments is one of the central questions in microbial ecology. High-throughput sequencing (HTS) studies are presently generating huge volumes of data to address this biogeographical topic. However, these studies are often focused on specific environment types or processes leading to the production of individual, unconnected datasets. The large amounts of legacy sequence data with associated metadata that exist can be harnessed to better place the genetic information found in these surveys into a wider environmental context. Here we introduce a software program, seqenv, to carry out precisely such a task. It automatically performs similarity searches of short sequences against the “nt” nucleotide database provided by NCBI and, out of every hit, extracts–if it is available–the textual metadata field. After collecting all the isolation sources from all the search results, we run a text mining algorithm to identify and parse words that are associated with the Environmental Ontology (EnvO) controlled vocabulary. This, in turn, enables us to determine both in which environments individual sequences or taxa have previously been observed and, by weighted summation of those results, to summarize complete samples. We present two demonstrative applications of seqenv to a survey of ammonia oxidizing archaea as well as to a plankton paleome dataset from the Black Sea. These demonstrate the ability of the tool to reveal novel patterns in HTS and its utility in the fields of environmental source tracking, paleontology, and studies of microbial biogeography. To install seqenv, go to: https://github.com/xapple/seqenv.
影响因子：
2.6
作者：
Couto, Jillian M.;Ijaz, Umer Zeeshan;Phoenix, Vernon R.;Schirmer, Melanie;Sloan, William T.
通讯作者：
Sloan, William T.