COMPUTER MANAGEMENT OF HIGH-RESOLUTION PHYSICAL DNA MAPS

高分辨率物理 DNA 图谱的计算机管理

• 批准号: 3333228
• 负责人: WILL GILLETT
• 金额: $ 24.42万
• 依托单位: WASHINGTON UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 1990
• 资助国家: 美国
• 起止时间: 1990-09-01 至 1994-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/3333228
• 关键词: DNA; computer graphics /printing; computer program /software; computer system design /evaluation; genetic mapping; information systems; restriction mapping

The overall goal of this project is to produce a hardware and software system for high-resolution (ca. 1 kb) DNA physical mapping, usable in a laboratory environment by a technician with no formal computer science background, This system will be applicable in a variety of DNA mapping environments, including mapping involving the human genome and the genomes of other higher organisms. It will be targeted to YAC technology and top- down mapping strategies. The specific aims are to: 1) develop data structures for manipulating and processing DNA restriction maps, starting with raw data and proceeding through the development of completed maps; 2) design and implement a computational database to be used as a repository of this date; 3) develop and implement a variety of algorithms for performing DNA mapping; 4) create an interactive editing system for creating and manipulating DNA restriction maps; and 5) integrate these and other components into a hardware and software DNA mapping system, usable in a biological laboratory by technical personnel untraned in computer science. The software will be designed with portability in mind, the final product being composed entirely of C code, supported only by SYBASE and X Windows. The software architecture will be "open" so that the incorporation of new mapping algorithms will not be an arduous task. The human interface to the system will include textual input, interactive menu control, graphical map display, and gel image display. The system will focus on clone-overlap mapping techniques and will constitute a software toolkit, providing multiple DNA mapping algorithms at three different levels of DNA mapping: clone ordering strategies, group boundary determination, and fragment order determination. The technicians will be able to select combinations of these algorithms to produce a mosaic of composite DNA mapping algorithms, adjusting to the specific mapping task. All of the algorithms will be cast within the framework of multiple- restriction-enzyme mapping. The framework allows fragment-size data from more than one restriction enzyme to be used, in order to reduce the uncertainty of clone overlap. In this framework, a linear increase in the experimental effort produces an exponential improvement in the quality of the maps produced.

该项目的总体目标是生产硬件和软件 高分辨率（约1 kb）DNA物理映射系统，可在 没有正规计算机科学的技术人员的实验室环境 背景，该系统将适用于多种DNA映射 环境，包括涉及人基因组和基因组的映射 其他更高的生物。 它将针对YAC技术和顶级技术 向下映射策略。 具体目的是：1）开发用于操纵和的数据结构 处理DNA限制图，从原始数据开始，然后进行程序 通过开发完整的地图； 2）设计和实施 计算数据库用作此日期的存储库； 3）发展 并实施多种执行DNA映射的算法； 4）创建 一种用于创建和操纵DNA限制的交互式编辑系统 地图； 5）将这些和其他组件集成到硬件中 软件DNA映射系统，可在生物实验室中使用 人事在计算机科学领域未经生动。 该软件将考虑到最终产品的可移植性设计 完全由C代码组成，仅由Sybase和X Windows支持。 软件体系结构将是“开放的”，以便结合新 映射算法将不是一项艰巨的任务。 人类的界面 系统将包括文本输入，交互式菜单控制，图形地图 显示和凝胶图像显示。 该系统将重点放在克隆越过映射技术上，并将 构成软件工具包，可在 三个不同级别的DNA映射：克隆订购策略，小组 边界确定和碎片顺序确定。 技术人员 将能够选择这些算法的组合来产生镶嵌物 复合DNA映射算法，调整为特定映射 任务。 所有算法将在多重框架内投放 限制 - 酶映射。 该框架允许从 为了减少多个限制酶 克隆重叠的不确定性。 在此框架中，线性增加 实验努力在质量方面产生了指数的提高 产生的地图。