Blastn is not working for short sequences?

Question

[Kumar]

I am trying to do blastn of two fasta files,which includes short sequence containing query fasta file (prom.fasta) and a bacterial draft genome (bac.fasta) as subject as follows,

prom.fasta
>og1_1
TTCGGTTCTAACGGCTGGGATTCGG

and

bac.fasta
>test
ATCAGCGTGGATTTGCCGGCGCCGGAATGGCCGATGATGCCGAATACTTCGCCGGGGCCG
ATCCGCAGATCGAGCGGATGCAGCGCCACGATCTGGCGACCGTCGACGGAATAGGACTTG
TGCAGGCGCTGAAACTGGATCACCGCGCGTGGCCGATTGGGGGGTCGTGAAGCCTACCAG
TCAATGTTTGGGGCCGTCATTCCATTCGGTTCTAACGGCTGGGATTCGGGAGTCGGGATT
GGGGATTCGCAAGAGCGGACGCCCTGGCCTTTGCGAATCCCGAGCCTCCAATCCCTAACG

I have used the following command for blastn analysis

blastn -query prom.fasta -subject bac.fasta -outfmt 6 -out result.xls

blastn gives no output though, the bac.fasta file having the exact similar sequence of prom.fasta. But, I do not know, why it is not giving output. could anyone help me to fix it.

Answer 1

[GenoMax]

You will have to use an additional parameter -task blastn-short for short sequences.

blastn-short    BLASTN program optimized for sequences shorter than 50 bases