hmm search target sequences

Question

[emertekin]

Hello,

I am trying to annotate fasta protein sequences in the Pfam database. I only want to get the best hit for each of my sequences. How can I do this with hmmsearch or phmmer?

Thank you

[ulah]

Is there a specific reason why you don't want to use the pfamscan.pl script provided on the pfam site? As far as I remember, it returns the best hit with default settings and it generally works quite well.