Functional annotation

[int11ap1]

Hi everybody,

I am designing a novel pipeline for processing metagenomic datasets. I'd like to use for functional annotation the following methods:

1) Full domain alignment methods (e.g. Pfam and TIGRFam)
2) Multiple motif methods (PRINTS)
3) Single motif methods (ProSite)

I guess that this list goes from very specific methods (1-->Pfam) to very sensitive methods (3-->ProSite), right? Thus, do you recommend me to analyse my sequences with Pfam first, then to analyse the remaining unannotated sequences with PRINTS and finishing with ProSite?

I cannot see the differences between Pfam and TIGRFam.

Any suggestion?
Thanks!

[bastianwur]

Is doing just all restricted by computational power? If not -> just all.