I am trying to identify DNA transposons in a newly sequenced insect. One of the ways to do this is by performing a tblastn of known DNA-transposase proteins towards the genome.
I therefore downloaded a .fasta file with DNA-transposase protein sequences and now want to blast them all to my genome, while selecting for hits that have a coverage of over 50% and a similarity of over 30%.
Then I wish to extract the best hits along with 5kb of flanking region into a .fasta file.
I am new to tblastn and can't figure out how I would go about doing that, can anyone lead me onto the right path?