Expanding Visualization and Analysis Tools for Comparative Microbial Ecology

海洋生物实验室（MBL）获得了一笔赠款，用于改进和开发数据库驱动的基于网络的工具，用于微生物生态学家分析和比较微生物群落。下一代DNA测序技术使生态学家能够在比以往任何时候都更深的深度探索微生物群落，发现新的生物体的速度比命名和接受更快。另一种独立于分类学的方法是使用SSU rRNA基因的区域对相似的DNA序列进行聚类，这现在是微生物生态学的标准方法。该网站将提供各种工具，使研究人员能够上传和聚类并行标签序列数据，并将提供一个新的聚类算法，结合已知的信息，测序错误率，进化率，和有关社区结构的信息。 具体而言，它将提供：（i）直接输入任何靶基因的平行序列，并对核糖体小亚基基因任何区域的序列进行分类鉴定;（ii）使用各种方法进行基于序列的动态聚类，包括将开发的一种新方法，该方法将实验变量和生物变量结合起来，不会夸大多样性值;以及（iii）改进的用于比较微生物群落的工具，其将基于序列的聚类与分类学和元数据联系起来。 该网站将免费提供，所有软件将开放源码，并尽可能独立于平台。下一代测序提供的数据远远超过许多研究人员的生物信息学能力。VAMPS网站（vamps.mbl.edu）已经证明在帮助来自世界各地的研究团队方面非常宝贵，包括NSF资助的研究项目，通过提供分析这些非常大且不断增长的数据集所需的生物信息学支持，数据库引擎和计算资源，并通过提供唯一公开的界面来直观地比较来自环境测序的微生物群落信息。 与MBL的研究生和博士后水平的微生物多样性夏季课程和环境科学本科学期合作，该项目将提供独特的教育机会，通过结合来自各种环境的数据，与国际海洋微生物普查数据集相关的元数据，其基于序列簇和基于分类学的分析和可视化工具的集成，以及项目开发人员提供的指导。

The Marine Biological Laboratory (MBL) is awarded a grant to improve and develop database-driven web-based tools for analysis and comparison of microbial communities for microbial ecologists. Next-generation DNA sequencing technologies allow ecologists to explore microbial communities at depths much greater than ever before uncovering new organisms faster than names can be given and accepted. The alternative taxonomic-independent approach of clustering similar DNA sequences using regions of the SSU rRNA gene is now standard for microbial ecology. The website will provide a variety of tools to allow researchers to upload and cluster massively-parallel tag sequence data and will provide a new clustering algorithm incorporating known information about sequencing error rates, rates of evolution, and information about community structure. Specifically, it will offer: (i) direct import of massively-parallel sequences of any targeted gene and taxonomic identification of sequences from any region of the ribosomal small-subunit gene; (ii) dynamic sequence-based clustering using a variety of methods, including a new method to be developed incorporating experimental and biological variables that does not inflate diversity values; and (iii) improved tools for comparing microbial communities that links sequence-based clusters to taxonomy and metadata. The website will be freely available, and all software will be open source and, to the extent possible, platform independent. Next-generation sequencing provides far more data than many researchers have the bioinformatics capacity to handle. The VAMPS website (vamps.mbl.edu) has already proven invaluable in aiding research teams from around the world, including NSF-funded research projects, by providing the bioinformatics support, database engine, and computational resources needed to analyze these very large and growing datasets, and by providing the only publicly-available interface for visually comparing microbial community information derived from environmental sequencing. In collaboration with the MBL's graduate and postdoctoral level Microbial Diversity summer course and undergraduate Semester in Environmental Science, this project will provide unique educational opportunities through its combination of data from a variety of environments, metadata associated with the International Census of Marine Microbes datasets, its integration of sequence cluster-based and taxonomy-based analytical and visualization tools, and the instruction provided by project developers.