[Computational-biology] Re: Point Specific Mutation Matrix vs. profile HMM ?

[harald]

Hello,

thanks a lot for your quick and detailed answers.
The papers comparing PSI-Blast and HMM profiles and the one about the 
statistical theory were pretty interesting.

But since the database, which I want to search for homologs is very big 
(~3 Mio. sequences), I think that a tool like hmmsearch would be too slow.

Kind regards,
Harald