UNDERSTANDING GENOMES BY THEIR REPEATED SEQUENCES

该提案概述了对以下几个问题的注释和说明工作 细菌基因组，包括胶囊红杆菌的基因组，现在是 在芝加哥大学的实验室里进行了测序 罗伯特·哈塞尔科恩博士的。这项工作的总体目标是创建一个 将用于商业查找的基因功能词典 病原菌基因组中的重要基因及其重要的工业意义 并尝试在人类基因组中进行功能分配。不寻常 DNA序列对称性，通常与调节 转录、复制和重组，将作为 全局批注工作。这些序列，包括倒置、镜像和 直接重复，在统计上被排除在编码区之外，并将被 用于消除虚假的开放阅读框架(ORF)并识别 重要的监管区域。这些退化序列的注记 将包括在一个称为喜鹊的自动标注系统中，该系统 由芝加哥大学开发。将确认开放源码边界 通过直接转录分析。重要的监管要素可以是 通过破坏这些序列中的对称性来测试功能 在体外检测转录异常。并行测序 其他菌株的基因组将允许 简并序列基序和重组点的比较。 暗示的简并序列将被测试重组生成活性 直接在一个简单的体内系统中，包括恢复抗生素 阻力标记物。对ORF测定和预测的见解 重组可能与复杂得多的类似任务相关 与人类基因组类似的序列。

This proposal outlines work on the annotation and elucidation of several bacterial genomes, including that of Rhodobacter capsulatus, now being sequenced at the University of Chicago in the laboratory in the laboratory of Dr. Robert Hasselkorn. The general aim of this work is to create a dictionary of gene functions that will be used to find commercially important genes in the genomes of pathogenic and industrially important organisms and attempt functional assignments in the human genome. Unusual DNA sequence symmetries, often implicated in the regulation of transcription, replication and recombination, will be mapped as part of a global annotation effort. These sequences, including inverted, mirror, and direct repeats, are statistically excluded from coding regions and will be used to eliminate spurious open reading frames (ORFs) and to identify important regulatory regions. Annotation of these degenerate sequences will be included in an automatic annotation system, called MAGPIE, being developed at the University of Chicago. ORF boundaries will be confirmed by direct transcriptional assays. Important regulatory elements can be tested for function by destroying the symmetries in these sequences and assaying for transcriptional anomalies in vitro. Parallel sequencing of the genomes of other strains of R. capsulatus will allow for the comparison of degenerate sequence motifs and recombination points. Suggestive degenerate sequences will be tested for recombinagenic activity directly in a simple in vivo system involving restoration of an antibiotic resistance marker. Insights into ORF determination and predicting recombination may be relevant to similar tasks in much more complicated sequences like the human genome.