blast short sequence with multiple N bases

Question

[Nicolas]

Hello!

I am trying to find a promoter inside a genome ensamble, I have the promoter sequence

GGTTGTNNNNNNNNNACAACC

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?

Thanks!

Edit = I increased evalue to 10, still no results

[Istvan Albert]

my feeling is that for blast to work properly you need to have a sufficient length of matching sequences. in your case perhaps try playing with the seed lengths and other parameters like that.

In general if you are looking for a pattern, you could try another tool that matches patterns rather than performs alignments.

https://bioinf.shenwei.me/seqkit/usage/#locate