Structural genome annotation and quantification of transcripts based on ultra-high-throughput transcriptome sequencing

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New ultra-high throughput sequencing technologies allow much cheaper and deeper sequencing of eukaryotic transcriptomes, termed RNA-Seq. The project aims at developing methods and software tools for the identification of complete transcript sets of protein-coding genes based on RNA-Seq and their accurate quantification in RNA-Seq samples. Based on one of the currently most accurate gene finders, AUGUSTUS, a strucural genome annotation pipeline will be developed that exploits RNA-Seq data simultaneously with other evidence sources. The aim is to generally and significantly increase the accuracy and comprehensiveness of structural genome annotation and to identify alternative splice forms more sensitively and confidently. Expression levels of transcripts will be estimated accurately to allow for the detection of changes in expression of genes or splice variants under different conditions. The universally applicable annotation pipeline will integrate RNA-Seq data from all new sequencing platforms and be freely available for independent use but will also be applied directly in some genome projects. If successful, this project would allow a significantly more accurate annotation and expression analysis in many eukaryotic genomes. It will therefore provide a better basis for other studies with potential biomedical, biotechnological or agricultural applications.