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Blastn for Short Sequences

Hi, I want to do Blastn for short sequences. e.g sequence with length of 11 nucleotides. Here is the sample.

test.fa

>Query_1
TGTTCAGCACT

$ blastn -db anyGenome -query test.fa -task "blastn-short" -output test_Output -outfmt 7 -word_size 7 -dust yes -evalue 1000 -ungapped

But Blast didn't return any hits. How I can make Blastn working for short nucleotides?

Thank you so much for your precious time.

Regards
Muhammad Shahbaz

blast alignment next-gen
• 5,277 views • link
updated by Ram Ram • written by shahbazmunir11 • shahbazmunir11

I tried matching short sequences (<10bp) with bowtie2. It seems to work. The multiple match limit maybe will have to adjusted and alignments would be in SAM format. Just in case.

• 1 views • link
written by microfuge microfuge

1 answer

Try shorter word size (minimum is 4) and try testing on a sequence from the db.

• 1 views • link
written by Asaf Asaf

You probably also need to increase the E-value threshold.

• 1 views • link
written by Jean-Karim Heriche Jean-Karim Heriche

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