hmmbuild

[HBotond]

Hello everybody!
I have a little problem with the hmmer.
First of all I downloaded a database which contains multiple protein alignments in a lot of separate multi fasta files. Now I want to use the hmmer’s hmmbuild tool to make HMM profile from these alignments and in the end I want to compere my own protein dataset to these profiles with the hmmschen tool.
Now my problem is that I don’t know how can I convert all of these fasta files to HMM profiles in on step. I can do separately but because I have a lot of fasta files this approach is impossible.
Have somebody got a good tip?
Thanks for all helps.

[GenoMax]

Are these sequences not represented in PFAM? You could download the HMM profiles from PFAM and do the search against those.

[HBotond]

I want to use the eggnog (Non-supervised Orthologous Groups) for a comparative genomic experiment. I want to sort my 6000 proteins to orthologous groups with the help of the hmm profiles generated from that database. Because these is huge database I want to automatize that step when I create hmm profiles from the aligned proteins.