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Development of Software for High-throughput PCR Design

高通量PCR设计软件的开发

基本信息

批准号：
6485101
负责人：
SVETLANA V MOROSYUK
金额：
$ 10.52万
依托单位：
DNA SOFTWARE, INC.
依托单位国家：
美国
项目类别：
财政年份：
2002
资助国家：
美国
起止时间：
2002-05-15 至 2002-11-14
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/6485101
关键词：
chemical kinetics chemical models computer program /software computer simulation computer system design /evaluation conformation high throughput technology nucleic acid hybridization nucleic acid structure oligonucleotides polymerase chain reaction thermodynamics

项目摘要

The mission of DNA Software Inc. is to enable the field of genomics by writing enterprise grade simulation software that incorporates state-of- the-art knowledge of the thermodynamics and kinetics of nucleic acid folding and hybridization. To accomplish this goal, we are developing core software called the Oligonucleotide Modeling Platform (OMP). OMP uses a standardized architecture, which allows it to accept different input and output data structures and to combine modules in a deployable fashion. OMP will reduce the development time and improve the reliability of any process involving oligonucleotide hybridization such as multiplex PCR, DNA sequencing, SNP detection assays, mRNA expression profiling, and a variety of chip array and microfluidics applications. This proposal focuses on the customization of OMP for automated high-throughput design of primers and in sillico optimization of reaction conditions for PCR in a variety of formats. The PCR OMP software will utilize a completely new approach for stimulating the product distribution after each step of PCR using both equilibrium and kinetic models of hybridization, target unfolding, and polymerase extension. The availability of the PCR OMP software is essential for the development of robust methods for low-cost high-throughput genotyping to enable disease association studies and personalized medicine. PROPOSED COMMERCIAL APPLICATIONS: Any company, research institution, laboratory, health-care organization, or government agency that uses PCR and/or DNA hybridization in general is a potential customer for PCR-OMP and other products of DNA Software Inc. PCR-OMP will be particularly useful to genomics companies that seek to make personalized medicine a reality.

DNA软件公司的使命是通过编写企业级模拟软件来实现基因组学领域，该软件结合了核酸折叠和杂交的热力学和动力学的最新知识。为了实现这一目标，我们正在开发称为寡核苷酸建模平台（OMP）的核心软件。OMP使用标准化的体系结构，这允许它接受不同的输入和输出数据结构，并以可部署的方式组合联合收割机模块。OMP将减少开发时间并提高涉及寡核苷酸杂交的任何过程的可靠性，例如多重PCR、DNA测序、SNP检测分析、mRNA表达谱以及各种芯片阵列和微流体应用。该提案的重点是定制OMP，用于引物的自动化高通量设计和各种形式的PCR反应条件的sillico优化。PCR OMP软件将利用一种全新的方法，使用杂交、靶解折叠和聚合酶延伸的平衡和动力学模型，在PCR的每个步骤后刺激产物分布。PCR OMP软件的可用性对于开发用于低成本高通量基因分型的稳健方法以实现疾病关联研究和个性化医疗至关重要。拟议的商业应用：任何使用PCR和/或DNA杂交的公司、研究机构、实验室、卫生保健组织或政府机构都是PCR-OMP和DNA软件公司其他产品的潜在客户。PCR-OMP将对那些寻求实现个性化医疗的基因组公司特别有用。