Comparative genomics with the VISTA/LAGAN computational system

描述（由申请人提供）：生物学家和基因组学家已广泛使用比较基因组学工具来了解人类和其他基因组的功能区域。该提案旨在创建一个集成的、易于使用的比较基因组学软件包，该软件包将在生物学家的个人机器或小型集群上运行，使生物医学研究人员能够研究感兴趣的基因组，即使它们无法通过任何主要的基因组浏览器获得。该软件包将基于两个最成功的比较基因组分析程序，VISTA基因组浏览器和LAGAN比对工具包，以前在我们小组开发，并已被数千名研究人员使用。该提案寻求支持，以创建一个稳定的独立软件系统，该系统基于对我们现有工具的改进和修改，研究人员可以在自己的实验室中使用，而无需将数据上传到任何服务器或使用预先计算的全基因组比对。这个软件包将结合先进的对齐和探索性可视化算法已经在我们的小组原型。该系统将为科学家提供选择参数的灵活性，大型数据集计算的轻松自动化以及数据的隐私性的显着组合，共同带来了密切分析单个基因或整个基因组的显着新颖能力。改进的VISTA/LAGAN工具将允许更好地使用比较基因组学来破译人类基因组中的生物医学相关特征。这些资源的目标用户将继续是生物医学研究人员，因此重点将放在生成工具和数据库上，这些工具和数据库将易于使用，结果易于解释。

DESCRIPTION (provided by applicant): Comparative genomics tools have become widely used by biologists and genomicists seeking to understand the functional regions of the human and other genomes. This proposal aims to create an integrated, easy-to-use comparative genomics package that will run on a biologist's personal machine or small cluster, allowing biomedical researchers to study genomes of interest even if they are not available through any of the major genome browsers. The package will be based on two of the most successful programs for comparative genome analysis, the VISTA Genome Browser and the LAGAN Alignment Toolkit, previously developed in our group and already used by thousands of investigators. This proposal seeks support to create a stable stand-alone software system, based on improvements and modifications to our current tools, which a researcher could use in his own laboratory, without being required to upload data to any server or use pre-computed whole genome alignments. This package will incorporate the advanced alignment and exploratory visualization algorithms already prototyped in our group. This system will give the scientist a remarkable combination of flexibility for choosing parameters, easy automation of the computation of large datasets, and privacy for their data, together resulting in the significant novel ability to closely analyze either individual genes or whole genomes. Improved VISTA/LAGAN tools will allow for enhanced use of comparative genomics for deciphering biomedically relevant features in the human genome. The target users of these resources will continue to be biomedical researchers, and thus focus will be placed on generating tools and databases that will be easy to use with readily interpretable results.