Pfam - get only one representative fasta sequence per family

Question

[Xylanaser]

Hey

can u help me with getting only one representative fasta sequence per family? Is there way to simply do that?

cheers

X

Answer 1

[jgreener]

It's not trivial. You could use the sequences from the trRosetta Pfam model set, which are representative of the family (download link).

We have a method for getting representative sequences in our paper if you are comfortable with using hmmsearch:

A representative target sequence was found for each family using hmmsearch to search the UniRef90 database with the Pfam HMM and taking the closest subsequence match by E-value.

[Xylanaser]

thanks for idea :)

Answer 2

[Mensur Dlakic]

hmmemit from the HHMer package will extract a consensus sequence for each HMM from Pfam:

hmmemit -c -o model.fasta model.hmm

Not only is it fast - can be done for the whole Pfam in under 2 minutes - but it is also objective because it gets the sequence directly from the model based on a simple majority rule. Keep in mind that consensus sequences generated this way may not exist in nature, although there will always be some real sequences that are very similar.