How to get hit DNA sequences from psi-tBLASTn?

Question

[carina2817]

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

[Joe]

You can’t do this from BLAST itself, AFAIK.

You will need to extract the IDs for all your hits from your blast result, then use blastdbcmd on your blast database to pull out the relevant hits that correspond to your list.