Hello, I'd like to reproduce the model's performance while generating MSAs locally.
I've got colabfold_search and mmseqs2 as the search tools, and uniref30_2302 and colabfold_envdb_202108 as DBs following the white paper.
But I don't know the exact commands and workflow for generating .a3m files the same way the authors did.
In particular, as I understand, I need to pair MSAs of different chains using taxonomy. But I'm not sure the current code includes such because I expect that there should be a file containing the taxonomy annotations, which I don't see:
We then assign taxonomy labels to all UniRef sequences using the taxonomy annotation provided by UniProt.
32 asked a similar question in addition to the confidentiality of the mmseqs server, but that part seems to have been missed out.
sangyeon-hits
commented
2 days ago
Hello, I'd like to reproduce the model's performance while generating MSAs locally.
I've got
colabfold_searchandmmseqs2as the search tools, anduniref30_2302andcolabfold_envdb_202108as DBs following the white paper.But I don't know the exact commands and workflow for generating
.a3mfiles the same way the authors did.In particular, as I understand, I need to pair MSAs of different chains using taxonomy. But I'm not sure the current code includes such because I expect that there should be a file containing the taxonomy annotations, which I don't see:
32 asked a similar question in addition to the confidentiality of the mmseqs server, but that part seems to have been missed out.