I've designed primers to identify a strain of interest.
Just to be sure that the primers matche only the genome of this strain and no other genomes, I am using blastn analysis.
My input file is :
>Seq_1 ATGTGCTAGCTATGGCG >Seq_2 GTCGGTAATCGATTCGA
And my database is a multifasta file containing several genomes including the genome of my strain of interest.
My command line is the following :
> blastn -query Sequences.fasta -db genomes.fasta -out Results_blastn.txt -outfmt 6 -evalue 0.1
The results file is blank.
I do not understand how I've got no results even on the genome of my strain of interest ...
Do someone have an idea on how I should proceed to fix this issue?
Thank you so much in advance for your much appreciated help!