Automatic Localization of Complete Protein Coding Genes in Eukaryotic Genomes

真核基因组中完整蛋白质编码基因的自动定位

• 批准号: 61416996
• 负责人: Professor Dr. Mario Stanke
• 金额: --
• 依托单位: Lehrstuhl für Bioinformatik
• 依托单位国家: 德国
• 项目类别: Research Grants
• 财政年份: 2007
• 资助国家: 德国
• 起止时间: 2006-12-31 至 2009-12-31
• 项目状态: 已结题
• 来源: https://gepris.dfg.de/gepris/projekt/61416996?language=en
• 关键词: Automatic; Localization; Complete; Protein; Coding

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.

该项目旨在开发一种基因查找工具，利用最近推出的下一代测序技术来实现更准确的基因组注释。新的超高通量测序技术可以对基因转录本进行更便宜、更广泛（“更深”）的测序，称为 RNA 测序。 RNA-Seq 为改进基因组注释程序开辟了新的机会，目前该程序仍然会错误预测许多基因结构，从而严重损害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。基于目前最准确的基因查找器之一 AUGUSTUS，将开发利用 RNA-Seq 数据的基因组注释管道。除了各种同源方法和蛋白质组学等已建立的证据类型之外，来自各种新测序平台的 RNA-Seq 数据也将被整合。目标是显着降低错误率并更灵敏、更自信地报告替代拼接形式。普遍适用的注释管道将免费供独立使用，但也可以直接应用于一些基因组项目。如果成功，该项目将能够通过转录组测序对许多真核基因组进行更准确的注释，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。