How to download the aligned fasta files from Pfam database?

[psp3dcg]

Thanks for the really nice package! However, when I want to test the package on more Pfam data, the downloaded fasta file from InterPro (https://www.ebi.ac.uk/interpro/entry/pfam/#table) is not aligned. For example (PF00020)

A0A060W133|unreviewed|Tumor necrosis factor receptor superfamily member 6|taxID:8022 MNKYTFLYILCILCTVRLTTPFNAERSSQDILITSKLRTKRQSCQDGTYQHEGMACCLCAAGQHLESHCSVSPEDGTCVY CEENRTYNSDPNSLDSCEPCTSCDSKANLEVEDRCTIFKDSVCRCQQGHYCNKGKEHCRACYPCTICSEEGIKVACSATN NTICHAFKEQGRNLAVVFVLTTVLLVLLVIIYLWRSNKYCFGPNGGLTELPNRSSEEMQPLRGVNLWPHLPDIAKTLGWR DMKQVAECSGMTHTAIESHQLNFPNDSQEQCSSLLRAWVEKEGMTTASVTLVQTLLRMKKKVKAEDIMAIISNKEDGVTG QNSGSGQV A0A060W225|unreviewed|TNFR-Cys domain-containing protein|taxID:8022 MFDKSMSNIGLHYMVVLLIWALNPMVAAQSGLKLTRTGGSVRNLTQRDISCQENLEYPHDNICCLNCLAGTYVKEYCTRA LERGTCEACEFDTYTEHGNGLRQCLKCTTCHSDQVTTKACTITQDRECRCKPGSFCAPDQACEVCKKCLRCEENEVRLKN CTATSNTVCKTRLPAPSTIPGTRPGTADIPLLHALLTPVYYYGLGFYCVLTQ

So how to get the aligned fasta like the example in your package? Thank U~

[pagnani]

Hi @psp3dcg. There are many options to have align sequences. This aspect goes beyond the package that assumes aligned inputs.

If you have a bunch of homologous sequences you could feed them to HHblits

[pagnani]

Closing as not planned

[psp3dcg]

OK， thank you~