Looking around for methodology on how to go about annotating a plant transcriptome. Whilst the information in papers tends to be simplified, and the internet does not really give a good simplied guide on how to go about this process, I've come here for a few simple answers.
1) What are the best databases available to annotate your Plant transcriptome with (de novo) assuming you are doing blastx on a stand a lone server and customized blastdb.
2) In regards to setting up your blastdb for blast x, what steps are involved. How do I for say, merge or parse several databases into 1 large custom database, so that the blastx can be performed once.
3) More broad question here; Once you get your annotation for the transcripts, how can you go about doing Pfam, Interpro?