Integration of Genetic Analysis and Map Generation with the E. coli Genetic Stock Center Database

该项目的目标是为大肠杆菌遗传资源中心数据库增加先进的功能，并扩展现有的数据库，以包括该中心现有的更多遗传信息。将特别强调开发和处理绘图信息的表示、计算和分析；使用和处理谱系数据；以及探索与专门提供与大肠杆菌数据库相关的信息的其他数据库的相互作用和可能的整合。拟议的工作将涉及扩展目前的设计和现有的数据库，并制定与其他数据库结合的计划。目前系统的设计和结构是在考虑到这些扩展功能的情况下开发的，因此可以完成必要的增加，而不需要放弃或重新设计任何先前的工作。该项目对于开发一个大型菌种数据库管理系统具有重要意义，该系统涉及复杂的遗传描述，每个菌种有多达20个遗传标记；提供了一种(以数据库格式)查询突变的类型和位置的手段，其范围从tRNA(抑制子)基因座的碱基对变化到基因之间的转座子或性别因素的插入，到基因内或基因间缺失，到染色体区域的倒位、转位或外延整合；开发遗传数据固有不确定性的表示方法；提供几乎任何遗传或菌株特征组合的检索能力，包括特定突变类型、特定基因或特定区域内的突变，带有或不带有标记的质粒，以及菌株属性，如性别或实验室来源；以及以关系格式提供生物和亚细胞水平的关键基因组信息，并具有与序列和其他物理数据库集成的能力。我们的作图功能方法的很大价值在于能够存储、分析和集成来自许多实验来源的数据以及汇总的图谱数据，并将图谱数据与我们广泛而准确的基因、等位基因和菌株数据库绑定在一起。这应该有助于检测，例如，图谱异常是菌株特异性的，或等位基因特异性的，或根据实验程序一致不同的。

The objective of this project is to add advanced features to the E. coli Genetic Stock Center database and to extend the current database to include additional genetic information currently available at the Center. Special emphasis will be put on developing and handling representation, computation, and analysis of mapping information; on the use and handling of pedigree data; and on exploration of interaction and possible integrations with other databases that specialize in information relevant to an E. coli database. The proposed work will involve extending the current design and the current database and developing plans for integration with other databases. The design and structure of the current system were developed with these expanded functions in mind, so that the necessary additions can be accomplished without requiring that any of the earlier work be discarded or redesigned. This project is significant in developing a database management system for a large strain collection involving complex genetic descriptions with as many as 20 genetic markers per strain; providing a means to query (in a database format) types and positions of mutations ranging from base pair changes in tRNA (suppressor) loci to insertion of transposons or sex factors between genes, to intragenic or intergenic deletions, to inversions, transpositions, or episome-integration of regions of the chromosome; developing representations of uncertainties inherent in genetic data; providing retrieval capability for virtually any combination of genetic or strain traits, including specific mutation types, mutations in specific genes or within specific regions, plasmids with or without markers, and strain attributes such as sex or lab of origin; and providing, in relational format, critical genome information at both the organismal and subcellular level, with capability of integration with sequence and other physical databases. Much of the value of our approach to the mapping function lies in the ability to store, analyze, and integrate data from many experimental sources as well as summary map data, and to have the map data tied to our extensive and accurate database of genes, alleles, and strains. This should facilitate detecting, for example, map anomalies that are strain specific, or allele- specific, or that consistently differ according to experimental procedure.