EAGER: Improved Computational Tools for Plant Gene Assembly and Synteny Detection

不断增加的基因组序列产生率将导致成千上万的基因组序列被确定。目前植物基因组装的自动化方法存在一定的固有弱点，导致许多基因组装错误，原因是无法准确检测内含子-外显子的真实边界，包括GC边界，无法检测n端外显子，以及相邻基因的不适当融合。专家手工注释通常可以克服这些限制，但是手工注释不能扩展到成千上万的基因。基因组计划通常只能声称人工检查了1000-3000个基因。在植物基因组中，这可能只占基因组中基因的3-10%。这个EAGER项目旨在提高自动化植物基因组装和注释，重点关注细胞色素P450基因，这是植物中最大的基因家族之一。准确的基因预测算法的成功实施和用于识别植物基因组中的同源基因（由全基因组复制事件产生的基因）的新工具的开发将对基因组注释产生变革性影响。本项目将为1名博士后提供国际跨学科培训机会。所有程序将作为一组可执行文件从ftp站点和通过项目网站提供，这两个站点都可以通过http://www.uthsc.edu/molecular_sciences/directories/faculty/d_nelson.php访问。源代码也将在此位置提供。

The ever-increasing rate of genome sequence production will result in literally thousands of genome sequences being determined. Current automated methods for plant gene assembly have certain inherent weaknesses that result in many incorrectly assembled genes due to inaccurate detection of true intron-exon boundaries including GC boundaries, inability to detect N-terminal exons, and inappropriate fusion of adjacent genes. Expert manual annotation can usually overcome these limitations, but manual annotation is not scalable to many thousands of genes. Genome projects generally are able to claim only 1000-3000 genes were manually checked. In plant genomes this may be only 3-10% of the genes in the genome. This EAGER project seeks to improve automated plant gene assembly and annotation with a focus on cytochrome P450 genes, which comprise one of the largest gene families in plants. Successful implementation of accurate gene prediction algorithms and the development of a novel tool for identifying ohnologs (genes created by whole genome duplication events) in plant genomes will have a transformative effect on genome annotation.This project will provide international cross-disciplinary training opportunities for one postdoctoral research associate. All programs will be available as a set of executable files from an ftp site and through the project website, both of which will be accessible via http://www.uthsc.edu/molecular_sciences/directories/faculty/d_nelson.php. The source code will also be made available at this location.