Pfam has the option to "Show all sequences with this architecture." How would I go about finding these from Pfam-A.full? I have quite a few queries to make.
I've been able to find individual domain hits with phmmer and hmmscan, but is it possible to find and align full order-sensitive multidomain sequences with the same architecture using the individual domain profiles with HMMER 3? Another tool?
1 answer
I ended up using the PhyloFacts curated database at http://phylogenomics.berkeley.edu/phylofacts/. They have a significant repository of curated architectural alignments from HMMs, as well as trees I was planning on building anyway. I'm getting roughly 70% hits from the database I'm using. The missing data can be assumed to be missing at random because of the nature of my other database. Saves significantly on CPU time and is well thought out, IMHO.
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