I have a protein alignment and want to look at conservation and PFAM protein domains at the same time. I have the protein fasta file exported from Ensembl and can see the conservation plot in Jalview. But there doesn't seem to exist a plugin to run my sequence(s) through Hmmer.
I don't know a lot about protein annotation, but it seems to me that this must be a very basic step for people that look on protein sequences: Get the protein domains and show the alignent. Do I really have to run Hmmer manually and write a perl script to export the Hmmer output to the Jalview feature format??
Any other ideas on how you usually approach this type of problem with other software (or other databases) are welcome!