This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Using BLAST Alignment with low sensitivity

Hello,

I would like to use BLAST with Low sensitivity(using DNA sequences). Wha't the best paramters should i choose? this is my command:

blastn -query query.fa -subject subject.fasta -out resultatblastn_cerevisae_real  -reward 5 -penalty -4 -gapopen 10 -gapextend 6 -evalue 1

should i change my parameters?

thanks for your help

blast alignment sequence
• 5,322 views • link
updated by Andrzej Zielezinski Andrzej Zielezinski • written by midox midox

What is your intent? By "low sensitivity" you mean finding only very similar sequences?

• 0 views • link
written by h.mon h.mon

no, it's the opposite. I want to find sequences with low similarity.

• 0 views • link
written by midox midox

You want a high sensitivity, low specificity blast, then.

• 0 views • link
written by h.mon h.mon

Hard to figure out exactly what you want but if it is not what @h.mon says then ..

relax the limits, set penalties to low values and collect all "hits" with -evalue set to 10. Then post-parse the results to select "hits" that fit your criteria for "low similarity".

• 0 views • link
written by GenoMax GenoMax

1 answer

If you want to find DNA sequences with low identity, you can descrease word_size from 10 to minimum or so (e.g., -word_size 4 or -word_size 6) and increase e-value from 10 to some big value (e.g., -evalue 1000). You can also turn off masking of low-complexity sequence regions (-dust no -soft_masking false).

blastn -task blastn -query query.fasta -db db.fasta -word_size 4 -evalue 1000 -dust no -soft_masking false

If you are looking for very short DNA sequences you can add the -task blastn-short parameter and play with scoring parameters.

blastn -task blastn-short -query query.fasta -db db.fasta -word_size 4 -evalue 1000 -dust no -soft_masking false -gapopen 3 -penalty -1
• 0 views • link
written by Andrzej Zielezinski Andrzej Zielezinski

You should add the -task blastn parameter (for finding sequences with low identity) even though your DNA sequence are longer than 50 bases. Because the default parameter is megablast, which is used to find very similar sequences.

• 0 views • link
written by Joe • Joe

Good point, I forgot about this. I updated my answer. Thanks.

• 0 views • link
written by Andrzej Zielezinski Andrzej Zielezinski

Log in to answer this question.

More posts like this