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库存中心数据库增加高级功能，并扩展现有数据库，以包括该中心目前可用的其他遗传信息。特别强调开发和处理地图信息的表示、计算和分析；论族谱数据的使用与处理探索与其他专门研究大肠杆菌数据库相关信息的数据库的交互和可能的集成。拟议的工作将涉及扩展目前的设计和目前的数据库，并制定与其他数据库整合的计划。当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添加，而不需要丢弃或重新设计任何先前的工作。本项目为大型菌株收集开发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，每个菌株多达20个遗传标记；提供一种方法来查询（以数据库格式）突变的类型和位置，从tRNA（抑制因子）位点的碱基对变化到基因间转座子或性别因子的插入，到基因内或基因间缺失，到反转、转位，或者染色体区域的片段整合；开发遗传数据中固有不确定性的表示；提供几乎任何遗传或菌株性状组合的检索能力，包括特定突变类型，特定基因或特定区域内的突变，带或不带标记的质粒，以及菌株属性，如性别或起源实验室；并以关系格式提供生物体和亚细胞水平的关键基因组信息，具有与序列和其他物理数据库集成的能力。我们的制图功能方法的大部分价值在于能够存储、分析和整合来自许多实验来源的数据以及汇总地图数据，并将地图数据与我们广泛而准确的基因、等位基因和菌株数据库联系起来。这将有助于检测，例如，毒株特异性或等位基因特异性的图谱异常，或根据实验程序始终不同的图谱异常。

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.