I was wondering if there is a good tool for annotation of eukaryotic genes obtained by gene prediction, for example, by Braker pipeline (or any other gene prediction pipeline for that matter)? By annotation I mean basically blasting and hmm-scanning putative proteins against various databases.
There is Trinotate and Dammit for transcripts, and both work reasonably well for assembled transcriptomes. However they use transdecoder, which doesn't seem to like transcripts generated from gene predictions, because they generally lack UTRs.
Any suggestions would be appreciated!