BLASTN for very short sequence

Question

[yas]

Hi everyone,

I want to blast a very short nucleotide sequence, TCACGGGTCGA (11bp) using the BLAST website, with e-value of 1000 and word size of 11.

However, I did not get any hits. Is there any suggestions on how I can fix this?

[GenoMax]

You are searching with a sequence that is at the lowest limit of BLAST. What database are you searching against? With that short a sequence you may simply want to look for pattern matches.

[yas]

I'm searching against the nucleotide collection (nr/nt) database. I actually want to look for organisms with that sequence (I got it from Bacillus amyloliquefaciens genome). May I know how to look for the pattern matches that you mentioned?

Answer 1

[Buffo]

You can try using the -task blastn-short

[GenoMax]

This setting is automatically applied on web blast which OP used.