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Pfam, DefenseCas, and AMRFinder make our lives easier. The hmm profiles already include GA values. Thus, in hmmsearch --cut_ga can be used as a parameter.
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COG is a little tricky. We need to figure out a cut-off for it.
So the immediate strategy would be adding a step to look for the presence of GA in the HMM file, if yes then add --cut_ga to the command.
Pfam, DefenseCas, and AMRFinder make our lives easier. The hmm profiles already include
GAvalues. Thus, inhmmsearch--cut_gacan be used as a parameter.COG is a little tricky. We need to figure out a cut-off for it.
So the immediate strategy would be adding a step to look for the presence of GA in the HMM file, if yes then add
--cut_gato the command.