Bioinformatics Tools Enabling Large-Scale DNA Barcoding

生物信息学工具实现大规模DNA条形码PI: Ion I. Mandoiu （University of Connecticut）合作PI: Bhaskar DasGupta (University of Illinois at Chicago), Mazhar Khan （University of Connecticut）高通量基因组技术的进步有望彻底改变21世纪的分类学，它使基于快速DNA分析对生活在地球上的大约2000万种物种进行自动鉴定成为可能。实现这一承诺提出了开发标准化分析平台的挑战，该平台可以以非常低的每次实验成本提供全面的物种鉴定。本研究项目的目标是开发新的生物信息学工具和设计方法，使基于通用DNA阵列的创新使用的大规模物种鉴定成为可能。这项工作将导致(1)有效的组合算法来解决大规模鉴定分析设计中出现的几个困难的优化问题，(2)优化两种经过验证的基因组技术（多重pcr和通用DNA标签阵列），(3)开发一种新的高通量基因组分析，(4)将上述优化整合在一个连贯的流程中，从而设计可扩展的物种鉴定分析的方法。(5)基于开发的优化算法的健壮的开源生物信息学工具，免费发布用于研究、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防御等领域产生深远的影响。其他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设施，作为未来研究、课程和课程开发的平台，指导本科生和研究生，以及促进研究活动的多样性。

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.