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

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
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written by erick_rc93 • erick_rc93

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.

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written by lieven.sterck lieven.sterck

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