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steineggerlab / foldseek

Foldseek enables fast and sensitive comparisons of large structure sets.
https://foldseek.com
GNU General Public License v3.0
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All-by-all alignment issue #192

Open daniel-dpq opened 9 months ago

daniel-dpq commented 9 months ago

I did an all-by-all alignment against my own database with the default setting. From my understanding, if there exists an alignment between query A and target B, an alignment between query B and query A should also exist. But in many cases this is not true. Any reasons for this or should I change some settings?

Thanks for any help.

martin-steinegger commented 8 months ago

Our scores are not symmetrical since our bias corrections are query structure dependent.