HIGH THROUGHPUT ANNOTATION OF GENOMIC DNA SEQUENCE

描述（申请人的摘要）：现在， 人类基因组已经掌握，目前正在努力提供 小鼠基因组，挑战在于识别由这些基因编码的基因。 基因组在这方面正在进行一些努力，包括我们自己使用ab 基因发现者和mRNA和EST形式的转录序列。 基因预测是识别基因的第一步。其他步骤是 预测这些基因的功能，并关联任何其他信息， 基因在哪里（以及何时）表达。拟议项目的目标 是提供一个公共数据库， 预测和相关注释。该项目将提供数据 整合使得对于相同基因的预测和注释（如定义的 通过共定位于相同的基因组位置）将被连接。关联 注释将扩展到包括函数预测和表达式 数据区.该数据库的预期用户是研究人员， 他们对基因的了解始于表达谱、cDNA或 基因位点或一般地搜索候选基因。原型 基因组序列的注释框架GAIA已经与 用于EST和mRNA、DoTS和基因整合的基因索引的原型， EpoDB.其结果是一个基于全局模式GUS的数据库， 来自GenBank、dbEST和SWISS-PROT的以序列为中心的条目， 以基因为中心的实体。此过程包括数据清理 并通过注释所得基因（mRNA和 蛋白质）。这个资源的第一次传递是在线的，带有专门的布尔查询 和集成的可视化工具，如www.allgenes.org。该资源将提供一个 整合了来自GenBank的已知和预测基因，基因发现者， 组装的EST和mRNA。本体将被用于构造注释 生物学概念和基因功能。基因表达信息将被 RAD（RNA Abstract Database）。没有其他公共资源 自然是存在的。将维护此资源的数据货币 每2-3个月定期更新一次。更新将包括整合 先前注释的基因与新获得的GenBank和dbEST条目 以及重新计算基因相似性、基因定位、组织分布， 基因功能开发了一个注释界面， 通过人工评估预测扩展计算分析， 基因及其功能。小鼠序列的辐射杂交作图数据 将像对人类EST所做的那样被纳入。基因之间的联系 将建立GUS中的基因表达数据和RAD中的基因表达数据。为应对 公共社区，对网络界面的查询将被合并和批量 为回应allgenes.org网站的用户而提供的文件。计划是 包括新重叠群按需注释。

DESCRIPTION (Applicant's abstract): Now that a working draft sequence of the human genome is in hand and an ongoing effort is in place to provide a draft of the mouse genome, the challenge is to identify the genes encoded by these genomes. Several efforts are underway in this regard including our own using ab initio gene finders and transcribed sequences in the form of mRNAs and ESTs. Gene prediction is the first step in identifying genes. Additional steps are to predict the function of those genes and associate any other information such as where (and when) the gene might be expressed. The goal of the proposed project is to provide a public database that will provide a central repository of gene predictions and associated annotation. The project will provide data integration such that predictions and annotations for the same gene (as defined by co-localizing to the same genomic location) will be linked. Associated annotation will be extended to include functional predictions and expression profiles. The intended users of the database are researchers seeking to extend their knowledge of a gene starting with an expression profile, a cDNA, or a genetic locus or to search generally for candidates genes. The prototype annotation framework for genomic sequence, GAIA, has been combined with prototypes for a gene index of ESTs and mRNAs, DoTS, and gene integration, EpoDB. The result is a database based on a global schema, GUS, that integrates sequence-centered entries from GenBank, dbEST, and SWISS-PROT and transforms the entries into gene-centered entities. This process includes data cleansing and adding value through annotation of the resultant genes (mRNAs and proteins). A first pass of this resource is on-line with ad hoc boolean queries and integrated visual tools as www.allgenes.org. The resource will provide an integrated set of known and predicted genes from GenBank, gene finders, and assembled ESTs and mRNA. Ontologies will be used to structure the annotations of biological concepts and gene function. Gene expression information will be augmented with RAD (RNA Abundance Database). No other public resource of this nature currently exists. Data currency of this resource will be maintained through periodic updates every 2-3 months. The updates will include integration of previously annotated genes with newly available GenBank and dbEST entries and recalculation of gene similarities, gene location, tissue distribution, and gene function. An annotation interface has been developed to complement and extend computational analysis through manual assessment of predictions for genes and their functions. Radiation hybrid mapping data for mouse sequences will be incorporated as has been done for human ESTs. Links between the genes in GUS and gene expression data in RAD will be established. To respond to the public community, queries to the web interface will be incorporated and bulk files provided in response to users of the allgenes.org site. Planned is the inclusion of on-demand annotation of new contigs.