I'am trying to run blastn to check if a sequence has a similar match within a database within a certain percent identity– to speed things up, I'd like blast to stop searching after finding a hit (it doesn't matter what the match is, just that it exists).so if there is a hit i got 1 and if there is not i got 1 .so in the end i get a matrice like in the picture !! Is there a parameter that does this? thank you my commande that iam trying to work with : for file in /scratch/Streptot.fa ; do
if [blastn -query $file -db /home/elgazel/recherche_virulance/Streptococcus_cbpA_DNA.fas -evalue 0.001 -outfmt 6 ] ; then echo "1" ; else echo "0" ; fi
done