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NextGenPartiGene: next generation transcriptome assembly annotation and exploitation toolkit

NextGenPartiGene：下一代转录组组装注释和开发工具包

基本信息

批准号：
BB/I023585/1
负责人：
Mark Blaxter
金额：
$ 15.79万
依托单位：
University of Edinburgh
依托单位国家：
英国
项目类别：
Research Grant
财政年份：
2011
资助国家：
英国
起止时间：
2011 至无数据
项目状态：
已结题

来源：
https://gtr.ukri.org/projects?ref=BB%2FI023585%2F1
关键词：
NextGenPartiGene next generation transcriptome assembly

项目摘要

Biologists have access to ever improving toolkits with which to ask probing questions of the natural world. One revolutionary development that has taken place over the last forty years is the advent of DNA sequencing. We now have the ability to decipher the genome sequence (or 'genetic blueprint') of any organism, and from this work out how they tick. About five years ago, this genomics revolution stepped up a gear, with the introduction of DNA sequencing technologies that increased the rate of genome sequencing, and reduced the cost, many, many fold. These 'next generation' technologies have suddenly made it possible for many researchers to start using genome sequencing in their work. However, as with any new technology, new solutions bring new problems. In the case of genome sequencing it is a 'rich person's' problem: researchers now can generate hundreds to thousands of times as much data as they used to, in a small fraction of the time, but they do not have the computer tools to process and understand it. The reduced cost of sequencing also means that many researchers who now can afford to use this technology do not have the long training required in computing to successfully analyse the floods of data. We propose to develop a set of easy-to-use tools, which we call NextGenPartiGene, using 'next generation' computing frameworks, that will alleviate this problem. We are focussing on the problem of working out what genes an organism is using (or 'expressing'), and what it is that these genes are likely to be doing. By sampling only the expressed genes of an organism (or a part of an organism, such as a leaf or a particular tissue type) it is possible to build up a detailed picture of the kinds of biochemical pathways the organism is running (what it can eat and what wastes it produces), and how experimental interventions change these pathways. We will build the NextGenPartiGene toolkit using an emerging model for such projects: the idea that much of the hard work is done by a server computer, running clever programmes behind the scenes, and that this server is driven by a client, accessed through a standard web browser. By building this client-server toolkit, we will be able to guide researchers with vast amounts of next-generation sequencing data down the best-practice, tried-and-tested paths to full and fruitful analysis. This means they will be able to extract maximum information from their data, and maximum value from their research funding. We will release the NextGenPartiGene tools as open-access software, so that others are both free to use it, and free to modify and improve it to fit their needs.

生物学家可以使用不断改进的工具箱，对自然界提出探索性的问题。在过去的40年里，发生了一个革命性的发展，那就是DNA测序的出现。我们现在有能力破译任何生物体的基因组序列（或“遗传蓝图”），并从中找出它们是如何工作的。大约五年前，这场基因组学革命加快了步伐，DNA测序技术的引入提高了基因组测序的速度，并降低了成本，很多很多倍。这些“下一代”技术突然使许多研究人员开始在他们的工作中使用基因组测序成为可能。然而，与任何新技术一样，新的解决方案也会带来新的问题。在基因组测序的情况下，这是一个“富人”的问题：研究人员现在可以在很短的时间内生成数百到数千倍的数据，但是他们没有计算机工具来处理和理解它。测序成本的降低也意味着许多现在能够负担得起使用这项技术的研究人员没有在计算方面所需的长期培训，成功地分析了大量的数据。我们建议开发一套易于使用的工具，我们称之为NextGenPartiGene，使用“下一代”计算框架，这将缓解这个问题。我们关注的问题是，弄清楚一个生物体正在使用（或“表达”）什么基因，以及这些基因可能在做什么。通过只对生物体（或生物体的一部分，如一片叶子或一种特定的组织类型）的表达基因进行采样，就有可能建立起生物体运行的各种生化途径的详细图像（它可以吃什么，产生什么废物），以及实验干预如何改变这些途径。我们将使用这类项目的新兴模型来构建NextGenPartiGene工具包：这种想法是，大部分艰苦的工作都是由服务器计算机完成的，在后台运行聪明的程序，并且这个服务器由客户端驱动，通过标准的Web浏览器访问。通过构建这个客户端-服务器工具包，我们将能够指导拥有大量下一代测序数据的研究人员沿着最佳实践、久经考验的路径进行全面和富有成效的分析。这意味着他们将能够从数据中提取最大的信息，并从研究资金中获得最大的价值。我们将NextGenPartiGene工具作为开放获取软件发布，这样其他人就可以自由使用它，并自由修改和改进它以满足他们的需求。

项目成果

期刊论文数量（7）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

afterParty: turning raw transcriptomes into permanent resources.

DOI：
10.1186/1471-2105-14-301
发表时间：
2013-10-07
期刊：
BMC bioinformatics
影响因子：
3
作者：
Jones M;Blaxter M
通讯作者：
Blaxter M

Blobology: exploring raw genome data for contaminants, symbionts and parasites using taxon-annotated GC-coverage plots.

DOI：
10.3389/fgene.2013.00237
发表时间：
2013
期刊：
Frontiers in genetics
影响因子：
3.7
作者：
Kumar S;Jones M;Koutsovoulos G;Clarke M;Blaxter M
通讯作者：
Blaxter M

Badger--an accessible genome exploration environment.

DOI：
10.1093/bioinformatics/btt466
发表时间：
2013-11-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
0
作者：
Elsworth B;Jones M;Blaxter M
通讯作者：
Blaxter M

The evolution of parasitism in Nematoda.

DOI：
10.1017/s0031182014000791
发表时间：
2015-02
期刊：
Parasitology
影响因子：
2.4
作者：
Blaxter M;Koutsovoulos G
通讯作者：
Koutsovoulos G

Formin Is Associated with Left-Right Asymmetry in the Pond Snail and the Frog.

DOI：
10.1016/j.cub.2015.12.071
发表时间：
2016-03-07
期刊：
Current biology : CB
影响因子：
0
作者：
Davison A;McDowell GS;Holden JM;Johnson HF;Koutsovoulos GD;Liu MM;Hulpiau P;Van Roy F;Wade CM;Banerjee R;Yang F;Chiba S;Davey JW;Jackson DJ;Levin M;Blaxter ML
通讯作者：
Blaxter ML