I am just wondering if we have any available tool to automatically confirm that a predicted gene model is correct or not based on RNA-Seq data? The only way to examine a gene model that I know is to visually compare the gene model and the RNA-read coverage on GBrowse. However, this method is time-consuming. If I have thousands of proteins which are candidates to be selected for further cloning, expression and biochemically characterization steps, and I have RNA-Seq read data of the genes encoding these proteins, could you please tell me how I can quickly know which proteins have correct gene models? Any ideas from you will be much highly appreciated.