Blastn is not working for short sequences?
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.
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1 answer
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
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