makeprofiledb -title cdd -in Cdd.pn -out cdd -threshold 9.82 -scale 100.0 -dbtype rps -index true
The parameter above is default, so the following command is OK, too. This is the sample for Cdd_NCBI.pn in large cdd database.
makeprofiledb -title cdd -in Cdd_NCBI.pn -out CDD
But My boss said we should use Cdd.pn instead!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
makeprofiledb -title cdd -in Cdd.pn -out CDD
Then, use rpsblast to search the protein:
rpsblast -query [intput-sequence-path] -db [database-path] -out [output-path] -evalue 0.01 -outfmt 7
-F: filter query sequence with SEG
-evalue : e-value 0.01 = 1e-2
-outfmt : 8 tabular output, -9 tabular output with comments
Reference:
http://blog.sciencenet.cn/blog-981687-725295.html
