Question: How does the algorithm scale with number of residues queried?

[dvanderwall]

Example test cases use 3-4 residues queried. What are the limitations to using more residues? Will there be higher false discovery? How to update parameters accordingly?

[khb7840]

By default, folddisco returns all partial matches so yes there would be more false discovery with more residues because the query grows quadratically. You can filter the result with the number of covered residues by applying --match 0,<number_of_residue_to_filter>. Or you can get results with 80% of residue coverage with --match 0,0.8. I'll update this in the documentation soon including the explanation on #8.