Entering edit mode
3.2 years ago
jihenelgazel5
•
0
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
