How pfam is made?

Question

[pooryamb]

Hi,

On the Pfam website, it is mentioned:

Blockquote Each Pfam family, often referred to as a Pfam-A entry, consists of a curated seed alignment containing a small set of representative members of the family, profile hidden Markov models (profile HMMs) built from the seed alignment, and an automatically generated full alignment, which contains all detectable protein sequences belonging to the family, as defined by profile HMM searches of primary sequence databases.

I wondered what is stored in the Pfam-A.hmm file we download from the Pfam website. Does it include the HMM that is drawn from seed alignment? Or the HMM from seed alignment is adjusted after searching the seed HMM against the sequence database?

Answer 1

[Mensur Dlakic]

profile hidden Markov models (profile HMMs) built from the seed alignment

It says it right there in the part you quoted.