LOGIC PROGRAMMING-BASED QUERY SYSTEM CHROMOSOMAL INFORMATION

由计算机科学家和计算机科学家组成的计算生物学协作室 每隔5个月在NIH或ANL聚集3-5天的生物学家 致力于开发一套新的集成工具 基因组信息的操纵已经被组织起来。发展 对这些信息学工具进行了集成组装和分析 在两次会议之间，数据继续通过互联网进行。最初的目标 这项研究的目的是建立必要的最低标准 描述可在逻辑上操纵的基因组图谱数据。结果 在这种合作努力中，已经开发了几个 原型演绎数据库系统：第一，大肠杆菌染色体 包含由NCBI的肯恩·陆克文提供的信息的查询系统 对于比对的DNA序列，识别出高分辨率的物理图谱 结构基因和比对的噬菌体图谱；第二，DCRT整合 收集鼠伤寒沙门氏菌的遗传和DNA序列数据；第三， 汉斯提供的S.pombe基因组信息的整合 英国伦敦帝国癌症研究基金会的Lehrach，包括 遗传连锁图谱，酵母人工染色体(YAC)和 粘粒杂交数据。每一个的对齐染色体信息 可以使用公共图形显示来查看这些原型中的 由阿贡国家实验室(ANL)为 合作。 我们开发的一项新技术--综合基因组数据库 ANL同事，允许将收集的基因和 多个生物体的物理数据。我们已经开发了许多工具 以促进基因组数据快速集成到该系统中。这个 这些原型数据表示系统中每一个的共同特征 是每个系统都使用逻辑编程语言PROLOG。我们可以的 快速开发对集成数据的复杂查询 所推断的复杂的相互关系的优势。例如, 在大肠杆菌系统中，找到最长的重复序列 在DNA螺旋的同一面上发现的任何基因都是一个简单的 序言查询。我们已经利用了这一高级查询功能 开始对选定基因组的全球组织进行分析。 转录因子结合位点分布的分析 相对于已知的启动子和基因，我们已经开始定义 代谢遗传调控的局部调控语法 小路。我们现在正在使用这些系统来关联这一安排 不同类型的遗传信息在每个 染色体类型。

A computational biology collaboratory of computer scientists and biologists that gathers every 5 months for 3-5 days at the NIH or ANL to work on the development of a new set of integrated tools for the manipulation of genomic information has been organized. Development of these informatics tools and assembly and analysis of the integrated data continues over the Internet between meetings. The initial objective of this research was to establish the minimal criteria necessary to describe genomic map data that may be logically manipulated. The result of this collaborative effort has been the development of several prototype deductive database systems: First, the E. coli chromosome query system that contains information provided by Kenn Rudd at NCBI for aligned DNA sequences, a high resolution physical map, identified structural genes, and an aligned phage map; second, DCRT- integrated collective genetic and DNA sequence data for S. typhimurium; third, an integration of the genome information for S. pombe provided by Hans Lehrach of the Imperial Cancer Research Fund, London, U.K., including a genetic linkage map, and Yeast Artifical Chromosome (YAC) and cosmid- hybridization data. The aligned chromosome information for each of these prototypes may be viewed using a common graphical display program developed at the Argonne National Laboratory (ANL) for the collaboratory. A new technology, the integrated Genome Database developed by our ANL colleagues, allows the integration of the collected genetic and physical data of multiple organisms. We have developed numerous tools to facilitate the rapid integration of genomic data into this system. The common feature of each of these prototype data representation systems is that each system uses the logic programming language Prolog. We can rapidly develop complex queries of the integrated data that take advantage of the complicated inter-relationships inferred. For example, in the E. coli system, finding the longest repeated sequences that are found on the same face of the DNA helix within any gene is a simple prolog query. We have taken advantage of this advanced query capacity to begin the analysis of the global organization of selected genomes. The analysis of the distribution of transcription factor binding sites relative to known promoters and genes has allowed us to begin defining local regulatory grammars for the genetic regulation of metabolic pathways. We are now using these systems to correlate the arrangement of different types of genetic information represented in each chromosome type.