BLASTN for very short sequence

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?

blastn

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written 3.3 years ago by yas •

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.

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written 3.3 years ago by GenoMax

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?

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written 3.3 years ago by yas •

1 answer

You can try using the -task blastn-short

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written 3.3 years ago by Buffo

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

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written 3.3 years ago by GenoMax

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