Downloading full alignments from Pfam
I used to download full alignments through the Pfam API, using the following URL scheme:
https://www.ebi.ac.uk/interpro/wwwapi/entry/pfam/PF00013/?annotation=alignment:full&download
However, for some months now, this URL returns 404 error. Here I am using PF00013 as an example, but the same happens for other domains.
On the other hand, attempting to download the seed alignments works fine:
https://www.ebi.ac.uk/interpro/wwwapi/entry/pfam/PF00013/?annotation=alignment:seed&download
Anyone knows how I should go about downloading the full alignments now?
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Not as convenient but the entire set of full alignments can be downloaded here: https://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.full.gz
This may be a question best sent to EBI help desk. If the seed alignments are working but full are not then there may be a bug that they need to fix. Please post their answer here when you get it.
I tried contacting Pfam, they replied that indeed there is an issue on their side with the full alignments, which should be repaired in the next release (sometime in the end of May)