Hello,

I am running psi-tBLASTn and I wonder if there is any tool to get hit DNA sequences from psi-tBLASTn in order to perform the reciprocal BLASTx .

I am using the following command to run psi-tblastn:

tblastn -num_threads 20 -db blastdb_P_bachei -in_pssm A_thaliana_mMit_psiblast_10it.chk -outfmt 6 -out test_P_bachei_tblastn.out

The query (-in_pssm A_thaliana_mMit_psiblast_10it.chk) is a checkpoint file (a Position Specific Scoring Matrix). When I ran simple tBLASTn I used the program biostar160470.jar to get the hit DNA seqences but it does not support a checkpoint file as query. Do you usually write your own scripts for this?

Thanks,

Paola