2018-06-13 Use rpsblast to sea

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.

makeprofiledb -title cdd -in Cdd_NCBI.pn -out cdd

But My boss said we should use Cdd instead!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

makeprofiledb -title cdd -in Cdd.pn -out cdd

Then, use rpsblast to search the protein:

rpsblast -i [intput-sequence-path] -d [database-path] -F T   -e 0.01 -m 9

-F filter query sequence with SEG
-e 0.01 = 1e-2
-m = 8 tabular output, -9 tabular output with comments

Reference:
http://blog.sciencenet.cn/blog-981687-725295.html