I am trying to find a promoter inside a genome ensamble, I have the promoter sequence
Whenever I try to find this sequences with the following code:
blastn -query=Prv211.fasta -subject=mtbgenome.fna -task=blastn-short -out=output.txt -evalue=10
, I have no matchs:
Database: User specified sequence set (Input: mtbgenome.fna). 1 sequences; 4,411,532 total letters Query= Length=21 ***** No hits found ***** Lambda K H 1.37 0.711 1.31 Gapped Lambda K H 1.37 0.711 1.31 Effective search space used: 35292152 Database: User specified sequence set (Input: mtbgenome.fna). Posted date: Unknown Number of letters in database: 4,411,532 Number of sequences in database: 1 Matrix: blastn matrix 1 -3 Gap Penalties: Existence: 5, Extension: 2
On the other hand, when I use the actual sequence of the promoter (with the actual bases instead of the Ns, it does find the promoter without problems)
Anyone knows why is this happening?
Edit = I increased evalue to 10, still no results