This is a test version of Biostars. For the public version, visit https://www.biostars.org.
How To Force Blastp To Display All The Possible Combination Of Alignments?

I want to use blastp to find out all the alignment among two fasta file.

Here is my command:

blastp -query "A.fasta" -subject "B.fasta" -evalue 1 -outfmt 6 > output.txt

I have already set the e-value tolerance to be 1, but there are still some alignments missing, is there anyway to force blastp to produce all the possible alignments?

blast alignment
• 3,433 views • link
updated by Michael Dondrup Michael Dondrup • written by Rein • Rein

Btw, how do you know, the alignments exist in the first place?

• 0 views • link
written by Michael Dondrup Michael Dondrup

1 answer

BLAST is a heuristic, it is not guaranteed to find all alignments. To increase sensitivity, try to decrease word_size (default is 3, try 2) and threshold parameters. Better, use FASTA or SSearch (Smith-Waterman) to get all local alignments which takes a lot of time. Oh, and set the evalue to 100, just in case ;)

• 1 views • link
written by Michael Dondrup Michael Dondrup

Thanks!! It is working, I found most of the missing alignments now, but what is the meaning of setting word_size to 2?

• 0 views • link
written by Rein • Rein

@Michael Dondrup Thanks!! It is working, I found most of the missing alignments now, but what is the meaning of setting word_size to 2?

• 0 views • link
written by Rein • Rein

Log in to answer this question.

More posts like this