Automatic Localization of Complete Protein Coding Genes in Eukaryotic Genomes

该项目旨在开发一种基因发现工具，利用最近引入的下一代测序技术，更准确地注释基因组。新的超高通量测序技术允许更便宜和更广泛（“更深”）的基因转录本测序，称为RNA-Seq。RNA-Seq为改进基因组注释程序提供了新的机会，目前这些程序仍然错误地预测了许多基因结构，这严重损害了预测基因的下游分析。RNA-Seq也带来了新的挑战，特别是因为序列片段通常比传统技术短得多。基于目前最精确的基因发现器之一AUGUSTUS，将开发利用RNA-Seq数据的基因组注释管道。除了已建立的证据类型（如各种同源性方法和蛋白质基因组学）外，还将整合来自各种新测序平台的RNA-Seq数据。目标是显著降低错误率，并更敏感和自信地报告可选择的剪接形式。普遍适用的注释管道将可以自由地独立使用，但也可以直接应用于一些基因组计划。如果成功，该项目将允许对许多真核生物基因组进行更准确的注释，并伴有转录组测序，从而为具有潜在生物医学，生物技术或农业应用的其他研究提供更好的基础。

The project aims at developing a gene finding tool that takes advantage of the recently introduced next-generation sequencing technologies for more accurate genome annotation. New ultra-high throughput sequencing technologies allow much cheaper and more extensive (’deeper’) sequencing of the transcripts of genes, termed RNA-Seq. RNA-Seq opens up new chances to improve genome annotation procedures, that currently still mispredict many gene structures which strongly impairs the downstream analysis of the predicted genes. RNA-Seq also poses new challenges, in particular because the sequence fragments are generally much shorter than in conventional technologies. Based on one of the currently most accurate gene finders, AUGUSTUS, a genome annotation pipeline that exploits RNA-Seq data will be developed. RNA-Seq data from the various new sequencing platforms will be integrated in addition to established evidence types such as various homology approaches and proteogenomics. The goal is to significantly reduce the error rate and to report alternative splice forms more sensitively and confidently. The universally applicable annotation pipeline will be freely available for independent use but also applied directly in some genome projects. If successful, this project would allow a significantly more accurate annotation of many eukaryotic genomes accompanied by transcriptome sequencing, and therefore provide a better basis for other studies with potential biomedical, biotechnological or agricultural applications.