Martin Steinegger

The E-value depends on two factors: the database size and the alignment score. As the database size increases, higher alignment scores are required to yield low E-values. If you prefer...

What kind of data do you try to cluster? You could try to set a `--tmscore-threshold`. But just a disclaimer, foldseek is not not meant to cluster huge set of...

` --alignment-type ` should work in the clustering. It also shows up in my help text. What version are you using. I recommend using the most recent version since I...

We don't have a straightforward method to achieve this, so your suggestion, @Yegor13, is accurate. You can simply mask the queryDB and queryDB_ss by substituting the desired letter with an...

I never tried to cluster such long sequences. Can you isolate the issue?

We calculated the TM-scores and LDDT scores using 3Di/AA structural alignments (`structurealign`). To obtain the TM-score and average LDDT score for the alignments we used `convertalis` modul.

We do have the scripts how to compute the purity per cluster here: https://github.com/steineggerlab/afdb-clusters-analysis

Please provide the pdb database and foldseek version used.

The server PDB database is not updated. This probably explains the differences. However, to check if your results are consistent with ours. Please check the following. Here is what I...

The differences in the database explain this. The PDB100 is not guaranteed to contain all the chains since it is clustered. Chains `1isv`, `1mc9`, and `1knm` are not cluster representatives...