Are there any good available programs/scripts for analyzing assembled transcripts? I imagine something like a script to blastn, blastx and tblastx each transcript and report the best hit. Something like that wouldn't be too hard to write, but I don't want to re-invent the wheel, and I also am concerned that sometimes the highest scoring hit reported by blast has a lot of gaps and is not the right result, while a lower scoring shorter hit is more likely correct, but the only way I can think of to accurately determine this is manually.

The genome I am interested in is poorly annotated, and particularly bad in my region of interest, so just using a reference gtf with my cufflinks transcripts would not be very helpful.