Is it possible to print DNA sequences of subject organism in tblastn?
I did tblastn analysis by following command
tblastn -query t3ss.fasta -subject org1.fasta -outfmt '6 qseqid qstart qend sseqid sstart send pident length evalue sseq' -out org1.xls
It prints the subject coordinates and translated amino acid sequences etc., Is there any way to print the DNA sequences of subject organism in tblastn?
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No. Not if you want to use functionality defined in
blast+.Sorry genomax, I did not get. What is called functionality in blast+
what genomax means to say is that you can not do this with blast+ itself (as in there is no option to request this directly form the blast output).
You could however parse the coordinates you get from the blast output and extract those regions from the original sequences if you want to obtain the DNA sequence from the matched region
You could use the accessions you get back with
blastdbcmdto retrieve the DNA sequences, but as mentioned, there’s no way to do this with blast itself.