How to set the number of mismatch in blastn
0
0
Entering edit mode
3 months ago

Hi everyone, I'm running blast nucleotide with word-size of 6 using the following command:

blastn -query 6452.fasta -db ref -out BlastResults.txt -num_threads 8 -outfmt '6 qseqid sseqid sseq' -word_size 6

Now I want to set the number of mismatch to 2 for the command. how should I add it? I added "-penalty 2" to command but it doesn't work!

Regards.

blastn mismatch penalty • 298 views
ADD COMMENT
0
Entering edit mode

Here's the error when I used "-penalty 2" for the command: Error: (CArgException::eConstraint) Argument "penalty". Illegal value, expected <=0: `2'

ADD REPLY
2
Entering edit mode

The penalties should be negative numbers (because they penalise the score), which is why 2 is not an allowed argument.

This isn't the same as the total number of mismatches, this is merely how much reduced an alignment score is, whenever a mismatch occurs.

I don't believe BLAST allows you to specify a particular number of mismatches - you'd have to post-filter your results or try a different approach.

ADD REPLY
0
Entering edit mode

what do you mean by post-filter?

ADD REPLY
0
Entering edit mode

Take the results from BLAST, and filter them after the fact to find alignments which only contain 1 or 2 gaps. This isn't an ideal approach though. You might have better luck with packages like fuzznuc depending on how similar you expect your results to be.

ADD REPLY

Login before adding your answer.

Traffic: 1626 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6