Pfam Superfamilies/Clans Alignments

Question

[JC]

Hello,

do you know how to download the Pfam superfamilies alignments in an amenable format (fasta, sto...). At Pfam, these alignments are in html format only.

For example, http://pfam.xfam.org/clan/CL0080#tabview=tab2 http://pfam.xfam.org/clan/CL0080/alignment

Regards Juan

Answer 1

[Mensur Dlakic]

It is not clear what you want, because Pfam has families and clans but not superfamilies.

Don't know how to download clan alignment or even if it is possible, because individual Pfam families that make up a clan are often very different in terms of length and are not easy to align globally.

To download alignments of individual families in stockholm format, say for PF04828, this would be the link:

https://pfam.xfam.org/family/PF04828/alignment/seed/format?format=stockholm&alnType=seed&order=t&case=l&gaps=default&download=1

For fasta format everything is the same but in the link change stockholm to fasta:

https://pfam.xfam.org/family/PF04828/alignment/seed/format?format=fasta&alnType=seed&order=t&case=l&gaps=default&download=1

Changing the PF... part in the link will download the corresponding family.

[JC]

Hello,

I meant clans, sorry. In the links that I sent on my first post you can see the alignment of a Pfam clan where all the families of the clan are aligned. Indeed, I compared this clan alingment with the individual alignments of each of the families of the clan and they have been clearly aligned to get the clan alignment.

I am interested in analysing sequence conservation at several positions of the alignment for each family but the html format that Pfam offers is not very useful . That's why I was wondering if it's possible to find it in a proper format somewhere else.

Regards Juan