2018-06-13 Use rpsblast to search Cdd database

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