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 用于高分辨率（约 1 kb）DNA 物理作图的系统，可用于 由没有正规计算机科学知识的技术人员提供的实验室环境 背景，该系统将适用于多种DNA作图 环境，包括涉及人类基因组和基因组的绘图 其他高等生物。 它将针对YAC技术和顶级- 向下映射策略。 具体目标是： 1）开发用于操作和处理的数据结构 处理 DNA 限制性图谱，从原始数据开始并继续 通过开发完整的地图； 2）设计并实现 用作该日期存储库的计算数据库； 3）开发 并实施多种算法来进行 DNA 作图； 4）创建 用于创建和操作 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 作图系统，可通过技术人员在生物实验室中使用 未经计算机科学训练的人员。 该软件的设计将考虑可移植性，最终产品 完全由 C 代码组成，仅受 SYBASE 和 X Windows 支持。 软件架构将是“开放的”，以便纳入新的 映射算法不会是一项艰巨的任务。 人机界面 系统将包括文本输入、交互式菜单控制、图形地图 显示器和凝胶图像显示器。 该系统将专注于克隆重叠映射技术，并将 构成一个软件工具包，提供多种DNA作图算法 DNA 作图的三个不同级别：克隆排序策略、组 边界确定和片段顺序确定。 技术人员 将能够选择这些算法的组合来生成马赛克 复合 DNA 映射算法，调整到特定的映射 任务。 所有算法都将在多重框架内进行铸造 限制性酶图谱。 该框架允许片段大小的数据 使用不止一种限制性内切酶，以减少 克隆重叠的不确定性。 在此框架下，线性增加 实验工作的质量呈指数级提高 制作的地图。