A k-mer-based search engine for sequencing databases

拥有生物测序数据的数据库保存着生物数据的宝库，这些数据可以用来帮助实验设计，并为新的生物项目找到相关的先前实验。然而，由于我们无法快速查询其中的原始数据，这些快速增长的档案严重未得到充分利用。就像搜索引擎改变了我们广泛而深入地在线获取信息的能力一样，搜索索引有可能彻底改变这些档案中排序数据的使用方式。在这个项目中，将开发能够快速和方便地访问这些数据库的方法。这将有助于生命科学数据的“谷歌化”，促进广泛的科学进步。此外，作为该项目的一部分，将开发一门“CS写作”课程以及一本算法概率分析练习册。将组织关于序列分析新方法的讲习班，并将为未被充分代表的本科生、研究生和博士后提供培训。该项目推动了生命科学中所有使用测序数据的领域的研究。它为测序实验数据库创建了强大的索引数据结构和查询算法。这可以允许生物学家查询测序数据库以找到表达特定感兴趣的转录本、显示两个转录本之间的差异表达水平、包含已知的剪接连接或基因融合、或包含感兴趣的小基因组的实验。该项目将促进生物学家能够对原始DNA和RNA测序实验的数据库执行许多生物陈述的查询。该项目的结果将在http://medvedevgroup.com/nsf-iibr-project.This上公布，该奖项反映了国家科学基金会的法定使命，并通过使用基金会的智力优势和更广泛的影响审查标准进行评估，被认为值得支持。

Databases with biological sequencing data hold a treasure trove of biological data that can be used to aid experimental design and find relevant prior experiments for new biological projects. However, these rapidly growing archives are heavily under-utilized due to our inability to rapidly query the raw data within them. Just as search engines transformed our ability to broadly and deeply access information online, search indices have the potential to revolutionize the ways in which sequencing data in these archives is used. In this project methods to enable fast and easy access to these databases will be developed. This will contribute to the “Googlification” of life-science data, spurring broad scientific advances. Additionally, as part of the project, a “Writing in CS” course as well as an exercise booklet for probabilistic analysis of algorithms will be developed. Workshops on emerging methods for sequence analysis will be organized, and training to underrepresented undergraduates, graduate students and postdocs will be provided. This project advances research across all areas of life science that work with sequencing data. It createspowerful indexing data structures and querying algorithms for databases of sequencing experiments. This can allow biologists to query sequencing databases to find experiments which express a certain transcript of interest, show differential levels of expression between two transcripts, contain a known splice junction or gene fusion, or contain a small genome of interest. This project will facilitate a biologist to be able to execute many biologically-stated queries on a database of raw DNA and RNA sequencing experiments. The results of this project will be available on http://medvedevgroup.com/nsf-iibr-project.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.