Download pfam sequence

Question

[saadleeshehreen]

Hi,

Does anyone know how to download only seed sequence from a pfam clan? This HTH clan has 340 seeds and I want to download only seeds not all sequences. And, need to download .fasta sequence rather alignment.

https://pfam.xfam.org/clan/HTH#tabview=tab2

Thanks in advance.

Cheers

Answer 1

[Mensur Dlakic]

Pfam seed alignments (Pfam-A.seed.gz) are here. You will have to extract the particular family or clan manually, and they will be in Stockholm format. From there, you go to FASTA using HMMer's utility esl-reformat.

esl-reformat -u fasta aln.sto > aln.fas