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

基因组序列产生的速度不断增加，将导致数以千计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些固有的缺陷，导致许多基因不能正确组装，这是因为不能准确地检测包括GC边界在内的真实内含子-外显子边界，无法检测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，但手动注释不能扩展到数千个基因。基因组计划通常能够声称只有1000-3000个基因被手动检查。在植物基因组中，这可能只占基因组中基因的3%-10%。这个迫切的项目旨在改善植物基因的自动化组装和注释，重点是细胞色素P450基因，它构成了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基因的新工具的开发将对基因组注释产生革命性的影响。该项目将为一名博士后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站点和项目网站获得，两者都可以通过http://www.uthsc.edu/molecular_sciences/directories/faculty/d_nelson.php.访问源代码也将在该位置提供。

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.