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

不断增加的基因组序列生产率将导致数以千计的基因组序列被确定。目前用于植物基因组装的自动化方法具有某些固有的弱点，其导致许多不正确组装的基因，这是由于不准确地检测真正的内含子-外显子边界（包括GC边界）、不能检测N-末端外显子以及相邻基因的不适当融合。专家手动注释通常可以克服这些限制，但手动注释无法扩展到数千个基因。基因组计划通常只能声称手动检查了1000-3000个基因。在植物基因组中，这可能仅占基因组中基因的3-10%。EAGER项目旨在提高植物基因的自动组装和注释，重点是细胞色素P450基因，该基因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鉴定植物基因组中ohnologs（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。该项目将为一名博士后研究助理提供国际跨学科培训机会。所有程序都将作为一组可执行文件从ftp网站和项目网站上提供，这两个网站都可以通过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.