How to create expandable profile databases?

[xvtyzn]

Hello.

I am currently running a variant impact prediction based on MSA. Recently, an preprint was published.

Alignment-based protein mutational landscape prediction: doing more with less, Marina Abakarova, Céline Marquet, Michael Rera, Burkhard Rost, Elodie Laine, bioRxiv 2022.12.13.520259; doi: https://doi.org/10.1101/2022.12.13.520259

This is that MSAs that can be created in colabfold using mmseqs2 are useful for variant impact prediction.

Now that we have our gene database, we would like to run this workflow using our own database. So we looked at the contents of the colabfold script and found that we need the expandable profile databases that are created by mmseqs2.

However, when I looked for how to create this database, I could not find it. I found the following command on the wiki, which converts already created expandable profile databases, right?

wget http://wwwuser.gwdg.de/~compbiol/colabfold/uniref30_2103.tar.gz
tar xzvf uniref30_2103.tar.gz
mmseqs tsv2exprofiledb uniref30_2103 uniref30_2103_db

Can you please tell me how to create it? Thank you in advance.

Keigo

[Chiyasa]

I come into the same problem. Do you have any solutions to it?

[xvtyzn]

Unfortunately, not yet. I leaved the project related to this issue. But I will try something for few days.

[dongzhuoer]

I also came into the same problem. The official wiki says: However, there were no further explanation until now.