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Published 20 hours ago • verified publisher icon soedinglab

Fix database size in mmseqs search

Open DuncanSussfeld opened this issue 4 years ago • 3 comments

I would like to specify in a mmseqs search command the effective size of a database, the way blastp allows with the -dbsize option. I have not been able to find an analogous option in the MMseqs help message, am I missing anything? Thanks

DuncanSussfeld avatar Nov 15 '21 09:11 DuncanSussfeld

Currently we don’t have an option like that. However, I encountered myself multiple cases where I could have used this feature. I can take a look into implementing this sometimes soonish (a bit busy right now though).

milot-mirdita avatar Nov 15 '21 12:11 milot-mirdita

Thank you for your reply. I look forward to hopefully being able to use this feature in the future!

DuncanSussfeld avatar Nov 15 '21 12:11 DuncanSussfeld

I'd love to see this option also, particularly in Foldseek (which I guess is somehow downstream of MMseqs2?).

seanrjohnson avatar Aug 28 '23 18:08 seanrjohnson