Blastn for Short Sequences

Question

[shahbazmunir11]

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

[microfuge]

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.

Answer 1

[Asaf]

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

[Jean-Karim Heriche]

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