Software and Server for Taxonomic Binning of Metagenomic Sequences

用于宏基因组序列分类分箱的软件和服务器

• 批准号: 0850256
• 负责人: Andrey Tovchigrechko
• 金额: $ 80.94万
• 依托单位: J. Craig Venter Institute, Inc.
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-04-15 至 2012-07-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0850256&HistoricalAwards=false
• 关键词: Software; Server; Taxonomic; Binning; Metagenomic

The J. Craig Venter Institute is awarded a grant to develop MGTAXA, a freely available software and a Web server for taxonomic classification of metagenomic sequences with machine learning techniques. This project will build three major components: 1) a toolbox for reliable assignment of species composition to large collections of unassembled environmental sequencing data, with automated and regular updates of databases and models; 2) a public Web server with a high-performance computational back-end that will let a wide community of biologists build classification models specific to their metagenomic samples; 3) an online instructional environment where students and educators will interactively combine several machine learning algorithms into graphically represented pipelines, apply them to sequences from annotated genomes and contribute to the re-usable repository of exercises and small research projects.The tools developed by this project will help both individual biologists and experienced bioinformatics teams analyze their metagenomic data for the discovery of novel genes, proteins, and metabolic pathways in microorganisms that cannot be grown in the laboratory conditions. This basic scientific research of our living environment will ultimately benefit the public by providing a necessary foundation for applied areas of study such as alternative energy sources and new medicines. The first question that needs to be answered by any metagenomic study is what species or higher taxonomic units are present in the sample, and to bin individual sequences to these units. The novel methodology of this project will require neither an existing homology to known sequences nor a preliminary assembly of individual fragments into longer segments. It also frees its users from a complexity of data management and installation that is beyond the abilities of smaller research groups.The free interactive online learning interface will provide both a hands-on experience and a curriculum development tool for students and teachers from colleges and high-schools, regardless of their geographical location. Source code of the tools developed by this project will be available at the open source development site SourceForge (http://sourceforge.net/projects/mgtaxa/). Web services will be available through a variety of venues: the JCVI web site (http://www.jcvi.org/) and the TeraGrid (http://www.teragrid.org). Certain tools will be submitted for inclusion into existing bioinformatics services Galaxy (http://galaxy.psu.edu) and CAMERA (http://camera.calit2.net).

J.克雷格文特尔研究所获得了一笔赠款，用于开发MGTAXA，这是一种免费提供的软件和网络服务器，用于利用机器学习技术对宏基因组序列进行分类。该项目将建立三个主要组成部分：1）一个工具箱，用于将物种组成可靠地分配给大量未组装的环境测序数据，并自动定期更新数据库和模型; 2）一个公共Web服务器，具有高性能的计算后端，可让广泛的生物学家建立针对其宏基因组样本的分类模型; 3）在线教学环境，其中学生和教育者将交互地将联合收割机若干机器学习算法组合成图形表示的流水线，将它们应用于注释基因组的序列，并有助于重新该项目开发的工具将帮助个人生物学家和有经验的生物信息学研究小组分析他们的宏基因组数据，以发现不能在实验室条件下生长的微生物中的新基因、蛋白质和代谢途径。这种对我们生活环境的基础科研最终将造福于公众，为替代能源和新药等应用研究领域提供必要的基础。任何宏基因组研究需要回答的第一个问题是样本中存在什么物种或更高的分类单位，并将个体序列与这些单位结合起来。该项目的新方法既不需要已知序列的现有同源性，也不需要将单个片段初步组装成更长的片段。它还将用户从复杂的数据管理和安装中解放出来，这超出了小型研究小组的能力。免费的交互式在线学习界面将为来自大学和高中的学生和教师提供实践经验和课程开发工具，无论他们位于何处。该项目开发的工具源代码可在开放源码开发网站SourceForge（http：//sourceforge.net/projects/mgtaxa/）上查阅。将通过各种渠道提供网络服务：JCVI网站（http：//www.jcvi.org/）和TeraGrid（http：www.teragrid.org）。将提交某些工具，供纳入现有的生物信息服务系统Galaxy（http：galaxy.psu.edu）和CAMERA（http：camera.calit2.net）。