I am wondering:
Are all the hits in out1.a3m included in out0.a3m?
If so, we only need run hhblits for a relatively large evalue, such as 100.0, then we select all the hits of particular smaller evalue, such as 1.0, from this result according to E-value column of result's hhr file.
Example: evalue0=1.0 evalue1=0.001 hhblits -i prot.fasta -o out0.hhr -ohhm out0.hhm -oa3m out0.a3m -e $evalue0 -d hhdb hhblits -i prot.fasta -o out1.hhr -ohhm out1.hhm -oa3m out1.a3m -e $evalue1 -d hhdb
I am wondering: Are all the hits in out1.a3m included in out0.a3m? If so, we only need run hhblits for a relatively large evalue, such as 100.0, then we select all the hits of particular smaller evalue, such as 1.0, from this result according to E-value column of result's hhr file.
Thank you very much in advance! Best wishes