soedinglab / MMseqs2

MMseqs2: ultra fast and sensitive search and clustering suite
https://mmseqs.com
GNU General Public License v3.0
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[Question] Is there any way to have at least one search result for each nucleotide sequence? #788

Open hwy7 opened 10 months ago

hwy7 commented 10 months ago

Expected Behavior

I want every query sequence to have at least one result returned.

Current Behavior

Both queryDB and targetDB are built using my own nucleotide data. Some sequences in queryDB have no results when I use search oreasy-search I want every query sequence to have at least one result returned.

milot-mirdita commented 10 months ago

You can disable the E-value threshold -e inf. However, this doesn't sounds like a biologically meaningful task, as it might return non-homologous sequences.

hwy7 commented 10 months ago

Thanks, it doesn't matter, I just need the similarity sequence