CDS transcript data and a reference genome: how to predict their 5' and 3' UTR?

Question

[khjadld]

Hello! everone. I have obtianed a CDS transcript data using BRAKER, and now I have a reference genome at hand. Who knows which software can acuratly predict their 5' and 3' UTR? Thanks in advance!

[Kevin Blighe]

Please shorten your question title

Edit: now shortened

[lieven.sterck]

does your CDS transcript data only contains the CDS (strictly) or is it rather (potentially) full length transcripts (== more than CDS thus) ?

[khjadld]

I used the protein data of a closely related species to train the my transcript data using AUGUSTUS in Braker2 pepline, but I did not add the parameter “UTR = on” when I run the Braker2.

[lieven.sterck]

to add UTRs to the CDSs, you would typically align the CDS sequences to the transcript data and consider all unmatched (up and downstream) part of the transcript which hits the CDS as UTR. It might makes sense to first collapse your transcript data to minimise redundancy.