Continued development and maintenance of the PHAST software for comparative genomics

持续开发和维护用于比较基因组学的 PHAST 软件

• 批准号: 9058580
• 负责人: Adam Charles Siepel
• 金额: $ 19.2万
• 依托单位: COLD SPRING HARBOR LABORATORY
• 依托单位国家: 美国
• 财政年份: 2015
• 资助国家: 美国
• 起止时间: 2015-04-24 至 2018-01-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9058580
• 关键词: Acceleration; Address; Area; Arthropods; Bioinformatics; Code; Communities; Comparative Genomic Analysis; Complex; Computer software; Computing Methodologies; Data Set; Development; Documentation; Elements; Environment; Eukaryota; Fellowship; Funding; Genome; Genomics; Grant; Human; Human Genetics; Imagery; Insecta; Investments; Life; Maintenance; Mammals; Manuals; Measures; Modeling; Molecular; Molecular Biology; Molecular Evolution; Phylogenetic Analysis; Process; Production; Publications; Research; Research Personnel; Resources; System; Testing; Time; Trees; Update; Vertebrates; Work; comparative; comparative genomics; computerized tools; falls; genome browser; genome sequencing; genomic data; improved; insight; novel; programs; reconstruction; software development; tool; vertebrate genome; web interface; whole genome

In recent years, there have been enormous investments in complete genome sequencing of species that fall close to one another on the tree of life, to permit comparative analyses on unprecedented scales. These analyses depend critically on the existence of rigorous and efficient computational tools. Our PHylogenetic Analysis with Space/Time models (PHAST) software package has developed into one of the most widely used toolsets in comparative genomics. PHAST contains the popular conservation scoring programs phastCons and phyloP, as well as a program for estimating the parameters of rich phylogenetic models, called phyloFit, and numerous supporting programs. We have developed and maintained PHAST for over a decade and it is now used by thousands of genomic researchers. Here we propose to continue our work maintaining, improving, and supporting PHAST, and to make several improvements needed for PHAST to keep abreast of recent developments in the field. Our proposal has two main aims: (1) to continue maintenance of support of PHAST, to make various improvements to our software development process, and to improve the accessibility of the software; and (2) to extend PHAST to support new data sets with hundreds to thousands of genome sequences and richer, more general alignment representations. We will closely coordinate our development of PHAST with the UCSC Genome Bioinformatics group's efforts on alignment, visualization, and genome reconstruction. Our software and browser tracks will remain freely available to the research community.

近年来，人们在完整基因组测序方面投入了大量资金。 生命之树上彼此接近的物种，以便进行比较分析 规模空前。这些分析关键取决于是否存在严格和 高效的计算工具。我们使用空间/时间模型进行系统发育分析 (PHAST) 软件包已发展成为比较领域中使用最广泛的工具集之一 基因组学。 PHAST 包含流行的保护评分程序 phastCons 和 phyloP， 以及一个用于估计丰富的系统发育模型参数的程序，称为 phyloFit， 以及众多的支持计划。我们开发和维护 PHAST 已超过一年 十年来，它现在被数千名基因组研究人员使用。在此我们建议继续 我们的工作维护、改进和支持 PHAST，并进行多项改进 PHAST 需要跟上该领域的最新发展。我们的建议有两个 主要目标：（1）继续维持对PHAST的支持，对 我们的软件开发流程，并提高软件的可访问性； (2) 至 扩展 PHAST 以支持具有数百到数千个基因组序列的新数据集， 更丰富、更通用的对齐表示。我们将密切配合我们的发展 PHAST 与 UCSC 基因组生物信息学小组在比对、可视化和 基因组重建。我们的软件和浏览器轨道将继续免费提供给 研究社区。