<p>Here's my working solution,</p>
<p>So I found a choice of parameters that resolves this, <code>-reward 3 -gapopen 5 -gapextend 5</code>.</p>

CC BY-SA 4.0
2021-10-08T17:17:27.337Z
2021-10-08T17:17:27.337Z
Set
<p>In my work I've found that in circumstances where there is a mismatch near the edges of the query sequence, blastn prefers to return a shorter contiguous alignment, rather than allowing for a mismatch near the 5' or 3' end of the query sequence.</p>
<p>For example, consider the subject sequence (bold indicates alignment with mismatch in brackets):</p>
<p>GACCAACCTG<strong>CTGGATCTGCTGATCGGCG[G]T</strong>TTGCGAAATA</p>
<p>and query sequence:</p>
<p>CTGGATCTGCTGATCGGCG[A]T</p>
<p>Blasting this will return the 19bp contiguous alignment upstream of the mismatch, rather than returning a 21bp alignment with a single mismatch at the G/A base at position 20 in the query.</p>
<p>I'm using the command line version of blastn, and I've tried messing with the penalties as well as setting <code>-task blastn-short</code>, but nothing seems to fix this issue.</p>
<p>I speculate that the various gap and mismatch penalties are working out such that a shorter contiguous alignment is preferred over a slightly longer alignment with a mismatch, but I haven't been able to figure out how to modify the penalties in such a way as to change this preference.</p>

CC BY-SA 4.0
2021-10-08T09:20:52.357Z
Nope, altering the weights is the solution as you said. So please do answer your own question —this a totally encouraged behaviour.
Matteo Ferla
<phylogenetics><blast><blastn>
blastn returning an inferior alignment
# blastn returning an inferior alignment

(Asked by: username_0 on 2021-10-07)

In my work I've found that in circumstances where there is a mismatch near the edges of the query sequence, blastn prefers to return a shorter contiguous alignment, rather than allowing for a mismatch near the 5' or 3' end of the query sequence.

For example, consider the subject sequence (bold indicates alignment with mismatch in brackets):

GACCAACCTG**CTGGATCTGCTGATCGGCG[G]T**TTGCGAAATA

and query sequence:

CTGGATCTGCTGATCGGCG[A]T

Blasting this will return the 19bp contiguous alignment upstream of the mismatch, rather than returning a 21bp alignment with a single mismatch at the G/A base at position 20 in the query.

I'm using the command line version of blastn, and I've tried messing with the penalties as well as setting `-task blastn-short`, but nothing seems to fix this issue.

I speculate that the various gap and mismatch penalties are working out such that a shorter contiguous alignment is preferred over a slightly longer alignment with a mismatch, but I haven't been able to figure out how to modify the penalties in such a way as to change this preference.

**Tags:** phylogenetics, blast, blastn
> **Comments:**
> **username_1**: Nope, altering the weights is the solution as you said. So please do answer your own question —this a totally encouraged behaviour.  

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## 1 answers

### Answer by username_0 on 2021-10-08. Score: 0 | Accepted answer

Here's my working solution,

So I found a choice of parameters that resolves this, `-reward 3 -gapopen 5 -gapextend 5`.


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