<p>It's easy; just use output <code>format 6</code>, this gives you a nice table that's easy to parse:</p>
<pre><code>blastn -db plasmid2.db -query plasmid1.fasta -evalue 1e-6 -outfmt &quot;6 pident evalue bitscore&quot;
</code></pre>
<p>I don't know what parameters you prefer.</p>
<pre><code>... &quot;6 pident evalue bitscore&quot; ...
</code></pre>
<p>You just edit the <code>pident</code>, <code>evalue</code> and <code>bitscore</code> above.  You might want to place <code>staxid</code> or something to tell you what it is. A selection of parameters are as follows:</p>
<blockquote>
<p>staxid ssciname qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore qcovs sstrand</p>
</blockquote>
<p>You might want to make the command a bit fancier</p>
<pre><code>blastn -db plasmid2.db -query plasmid1.fasta -evalue 1e-7 -outfmt &quot;6 pident evalue bitscore&quot; | sort | uniq -c | sort -n &gt;&gt; myplasmid.txt
</code></pre>

CC BY-SA 4.0
2023-04-12T13:13:33.780Z
2023-04-12T16:20:13.797Z
2023-04-12T16:20:13.797Z
M__
<p>I have 96  fasta files (A1, A2, A3...) from one  plasmid assembly pipeline, and I have another 96 fasta  files (B1, B2, B3 ...) from another plasmid assembly pipeline.
I would like to compare pair wise (A1 to B1, A2 to B2, A3 to B3 etc) and collect some metrics to see how this two assembly method differs.</p>
<p>I am thinking of doing blastn -query A1 -subject B1, but this created a lot visual alignment, rather than detailed align metrics.</p>
<p>Thank you for your suggestions.</p>

CC BY-SA 4.0
2023-04-12T11:26:17.667Z
OK, I think maybe I will just stay with blastn and do this: blastn -query A1 -subject B1 |grep -E "Score|Identities|Strand" >res_A1_B1
 Then I will get report like this  in res_A1_B1, Score = 1.048e+04 bits (5674),  Expect = 0.0
 Identities = 5674/5674 (100%), Gaps = 0/5674 (0%)
 Strand=Plus/Minus
 I can further collect them into tables.
cautree
<phylogenetics><fasta><phylogeny><assembly><blast>
compare fasta sequences in pairs and collect metrics
# compare fasta sequences in pairs and collect metrics

(Asked by: username_0 on 2023-04-12)

I have 96 fasta files (A1, A2, A3...) from one plasmid assembly pipeline, and I have another 96 fasta files (B1, B2, B3 ...) from another plasmid assembly pipeline.
I would like to compare pair wise (A1 to B1, A2 to B2, A3 to B3 etc) and collect some metrics to see how this two assembly method differs.

I am thinking of doing blastn -query A1 -subject B1, but this created a lot visual alignment, rather than detailed align metrics.

Thank you for your suggestions.

**Tags:** phylogenetics, fasta, phylogeny, assembly, blast
> **Comments:**
> **username_0**: OK, I think maybe I will just stay with blastn and do this: blastn -query A1 -subject B1 |grep -E "Score|Identities|Strand" >res_A1_B1  Then I will get report like this  in res_A1_B1, Score = 1.048e+04 bits (5674),  Expect = 0.0  Identities = 5674/5674 (100%), Gaps = 0/5674 (0%)  Strand=Plus/Minus  I can further collect them into tables.  

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## 1 answers

### Answer by username_1 on 2023-04-12. Score: 3 | Accepted answer

It's easy; just use output format 6, this gives you a nice table that's easy to parse:
blastn -db plasmid2.db -query plasmid1.fasta -evalue 1e-6 -outfmt "6 pident evalue bitscore"

I don't know what parameters you prefer.
... "6 pident evalue bitscore" ...

You just edit the pident, evalue and bitscore above.  You might want to place staxid or something to tell you what it is. A selection of parameters are as follows:

staxid ssciname qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore qcovs sstrand

You might want to make the command a bit fancier
blastn -db plasmid2.db -query plasmid1.fasta -evalue 1e-7 -outfmt "6 pident evalue bitscore" | sort | uniq -c | sort -n >> myplasmid.txt


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