Bioinformatics Tools Enabling Large-Scale DNA Barcoding

生物信息学工具实现大规模 DNA 条形码

• 批准号: 0543365
• 负责人: Ion Mandoiu
• 金额: $ 39.96万
• 依托单位: University of Connecticut
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2006
• 资助国家: 美国
• 起止时间: 2006-07-01 至 2010-06-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0543365&HistoricalAwards=false
• 关键词: Bioinformatics; Tools; Enabling; Large; Scale

Bioinformatics Tools Enabling Large-Scale DNA Barcoding PI: Ion I. Mandoiu (University of Connecticut) Co-PIs: Bhaskar DasGupta (University of Illinois at Chicago), Mazhar Khan (University of Connecticut) Advances in high-throughput genomic technologies promise to revolutionize 21st century taxonomy by making possible automated identification of the estimated 20 million of species living on Earth based on rapid DNA analysis. Fulfilling this promise raises the challenge of developing a standardized analysis platform that provides comprehensive species identification at very low cost per experiment. The goal of this research project is to develop novel bioinformatics tools and design methodologies enabling large-scale species identification based on innovative uses of universal DNA arrays. The work will lead to (1) efficient combinatorial algorithms for several difficult optimization problems arising in the design of large-scale identification assays, (2) optimization of two proven genomic technologies (multiplex-PCR and universal DNA tag arrays), (3) the development of a novel high-throughput genomic assay, (4) methodologies for integrating the above optimizations in a coherent flow enabling the design of scalable species identification assays, and (5) robust open source bioinformatics tools based on developed optimization algorithms, released free of charge for research, academic and non-profit purposes. By enabling large-scale genomic-based species identification, the research will have far reaching impacts in areas ranging from medicine and agriculture to biodiversity research and biodefense. Additional broader impacts include improving scientific infrastructure by timely dissemination of open source software tools and benchmark datasets as a platform for future research, course and curriculum development, mentoring of undergraduate and graduate students, and promoting diversity in research activities.

生物信息学工具实现大规模DNA条形码PI：I. I. Mandoiu（康涅狄格大学）Co-Pis：Bhaskar Dasgupta（伊利诺伊州伊利诺伊大学的Mazhar Khan（Mazhar Khan），Mazhar Khan（康涅狄格大学）在康涅狄格大学（University of Connection of Center Inter Inter Inter Inter Inter Interymitized niver Interymitized niver Interymatized Interymitized sensposity knemant of革命范围）的进步，以革命性的统一，以革命性地统治该范围，从而使估计性革命性变化范围，从基于快速DNA分析。实现这一诺言，提出了开发标准化分析平台的挑战，该平台以每次实验的成本非常低，提供全面的物种识别。该研究项目的目的是开发新型的生物信息学工具和设计方法，从而基于通用DNA阵列的创新用途实现大规模的物种识别。这项工作将导致（1）有效的组合算法，用于在大规模识别测定的设计时引起的几个困难优化问题，（（2）优化两种经过验证的基因组技术（多重PCR和通用DNA TAG阵列），（3）用于整合上述高通量启用的方法，（4）在上述过程中的开发，（4）在上述方法中的开发，（4）在上面的延展性指定，以上述为基础，（4）在上面的延展性序列，以上述为基础，（4）以上定义了一定的指定。识别测定法，以及（5）基于开发的优化算法的强大开源生物信息学工具，用于研究，学术和非营利目的。通过实现大规模的基于基因组的物种鉴定，该研究将在从医学和农业到生物多样性研究和生物形式的领域产生遥远的影响。更广泛的影响包括通过及时传播开源软件工具和基准数据集来改善科学基础架构，作为未来研究，课程和课程发展的平台，指导本科生和研究生，并促进研究活动的多样性。