DATABASE AND COMPUTER TOOLS FOR GENOME MAPPING

我们的观点是，一个完整的基因组数据库必须包含 至少包括以下数据：1.分子图谱信息， 从细胞遗传学分辨率向下分层排列 单个核苷酸;2.遗传信息，分层排列 从连锁分析排序的基因座到等位基因和突变基因 表型变异;3.关于基因表达的生化信息 图案（例如，组织和细胞周期特异性）、基因表达 调节（例如，转录激活），信号转导（例如， 上游调节子/下游靶点）和蛋白质活性调节 (e.g.,磷酸化）。为了使这些信息对规划有用， 实验的关键发现，计算机系统必须有以下几点 特点：4.及时、直接地获取所有相关的人类基因组数据 和所有模式生物，以高度特异性的方式， 检索感兴趣的数据（访问的必然结果是 能够直接将相同类型的数据提交给相同的、实际的或 虚拟数据库;这允许数据在 调查员）;5.用于操作和分析数据的交互式工具 以及用于探索系统内的数据元素之间的关系 (e.g.能够使用计算机算法绘制新确定的cDNA 序列（或限制酶消化的质粒）与现有的基因组 由一个大的限制性内切酶提供的序列（或预测的限制性位点）， 测序中心）;6.能够收集和存储 相关数据（单个项目），以便于分析， 与参与该项目的同事（来自博士后和 同一实验室的技术人员到不同机构的小组）;7.的 构建系统的软件必须能够快速更改， 扩展，以便能够处理对现有数据理解的变化 以及基因组学新技术的发展 调查;8.该软件必须在技术上强大，但相对 易于使用，统一的一般操作，比如说，像麦金塔电脑 或强大的文字处理器。我们已经开发出一种先进的原型， 系统具有上述基本功能。这一制度 在多个地点进行测试和评估。在下一个预算期间， 我们需要优化系统的性能， 解决上述八个问题的软件和战略。

It is our view that for a genomic database to be complete it must contain at least the following data:1. Molecular mapping information, hierarchically (in resolution) arranged from cytogenetic resolution down to individual nucleotides;2. Genetic information, hierarchically arranged from loci ordered by linkage analysis down to allelic and mutational phenotypic variation;3. Biochemical information regarding gene expression patterns (e.g., tissue and cell cycle specificity), gene expression regulation (e.g., transcription activation), signal transduction (e.g. upstream regulators/downstream targets), and protein activity regulation (e.g., phosphorylation).For this information to be useful for planning experiments key to discovery, the computer system must have the following features:4. Timely, direct access to all relevant genomic data from human and all model organisms, in a highly specific manner such that only those data that are of interest are retrieved (the corollary of access is the ability to directly submit the same type of data to the same, actual or virtual database; this allows rapid flow of data from and to investigators);5. Interactive tools for manipulating and analyzing data and for exploring relationships between data elements within the system (e.g. be able to map, using a computer algorithm, a newly determined cDNA sequence (or restriction enzyme digested plasmid) to an existing genomic sequence (or predIcted restriction sites) provided by one of the large sequencing centers);6. Ability to collect and store logical collections of related data (individual projects) in a way that facilitates analysis and for sharing with colleagues involved in the project (from postdocs and technicians in the same lab to groups at different institutions);7. The software on which the system is built must be capable of rapid change and extension, to be able to handle changes in understanding of existing data and the development of new technologies involved in genomic investigations;8. The software must be technically powerful but relatively easy to use, uniform in general operation, say, like a Macintosh computer or a powerful word processor.We have developed an advanced prototype of a system that has the basic functionality outlined above. This system is in test and evaluation at several locations. During the next budget period, we need to optimize the performance of the system and to develop new software and strategies to address the eight issues listed above.