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EddyRivasLab / hmmer

HMMER: biological sequence analysis using profile HMMs
http://hmmer.org
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Is it possible to speed up phmmer searches with makehmmerdb ? #303

Closed gciaberi closed 1 year ago

gciaberi commented 1 year ago

In the documentation about makehmmerdb, it says "... is used to create a binary file from a DNA sequence file." Can it be used for protein databases ? I've tried running it with default parameters on Uniref90, but after some time the process stops and I get "Killed" in my terminal.

Are there other ways of speeding up search speed with phmmer beyond the --cpu option ?

cryptogenomicon commented 1 year ago

From the documentation:

makehmmerdb is used to create a binary file from a DNA sequence file. This binary file 
may be used as a target database for the DNA search tool nhmmer.

No, it doesn't work for phmmer or programs other than nhmmer.