blastn with short sequences gives no results in the corresponding genome

Question

[A_heath]

Hi all,

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!

Audrey

[Joe]

You might want to take a look specifically at PrimerBlast (https://www.ncbi.nlm.nih.gov/tools/primer-blast/) which is designed specifically for this.

Answer 1

[Andrzej Zielezinski]

Just add -task blastn-short to your command. By default, blastn uses megablast (optimized for highly similar long sequences).

[A_heath]

Indeed, it works better now ... Thank you so much for your help a.zielezinski!