Open fteufel opened 2 years ago
That seems about right? It aligned two residues successfully (from 83 to 84). You might want to demand some coverage thresholds (-c/-cov-mode
) or a minimum aln length threshold (--min-aln-len
).
Thanks for pointing out this was correct! I did not realize that this was just a denominator issue. --seq-id-mode
was what I needed to change, as the default does not make much sense for this application.
Hi,
I'm using MMseqs2 for all-vs-all alignments. As indicated in the user guide pdf, I'm using the bash script to perform a fake prefiltering step before aligning. That seems to work, as all alignments are computed, but the results are a bit unexpected:
I didn't change much of the defaults
The second alignment's
fident
makes no sense to me. I understand that the e-value is high too, but I really want all pairwise % identities returned so I don't use it for filtering. Do I need to use a different configuration to make this work, or is mmseqs2 just not suitable for this all-vs-all identity task?