Use the Pfam database and a local database together to find protein domains

0

Entering edit mode

6.0 years ago

erick_rc93 ▴ 30

I have downloaded the Pfam-A database to find protein domains, but I'd like to add new domains that I have build with HMMER, but I don't know how to use both database together. For the new database, I have download the protein sequences in amino acids in a single fasta file, then I aligned the sequences with mafft and after that, I used the next hmmer program

hmmbuild proteoms_1_aln_hmm.fasta proteins_1_aln.fasta

I don't know which are the next steps.

genome alignment gene • 1.3k views

ADD COMMENT • link 6.0 years ago by erick_rc93 ▴ 30

1

Entering edit mode

Is there any particular reason you want to use them both together? Would you be OK with using them separately and merging the results if need be?

If so: simply do a screen with your custom build profiles using hmmsearch , this is without going into detail, roughly similar as what the Pfam-A screening would do.

ADD REPLY • link 6.0 years ago by lieven.sterck 15k

Login before adding your answer.