You can train Augustus with that information

You might also want to consider MAKER (which can use different data sources) or Exonerate (doesn't use different data sources, but can be tested for making gene annotations)

If you're not a fan of using the command line, you could try GenSAS. I saw their presentation at PAG and from what I gather you can carry out gene annotation through their website by just supplying the raw sequencing files. They integrate popular tools, so you can run everything through them.

I'm not sure if this is what you're looking for - your question doesn't state whether you already have the transcriptome etc files and want to use them to annotate a genome sequence, or whether you're looking for these files to help you annotate genes.