<p>You can extract fasta sequence from a blastdb constructed from a fasta file using blastdbcmd which should be installed when you install blast/makeblastdb.</p>

<pre><code>blastdbcmd -entry all -db &lt;database label&gt; -out &lt;outfile&gt;
</code></pre>

<p>If you had a database called <code>my_database</code> which contained the files:</p>

<ul>
<li><code>my_database.nhr</code> </li>
<li><code>my_database.nsq</code> </li>
<li><code>my_database.nin</code></li>
</ul>

<p>and you wanted your fasta output file to be called <code>reference.fasta</code> you would run the following:</p>

<pre><code>blastdbcmd -entry all -db my_database -out reference.fasta
</code></pre>

CC BY-SA 3.0
2017-06-19T15:25:03.003Z
2017-06-19T15:25:03.003Z
amblina
<p>How to extract the sequence used to create a blast database.  This is useful when you download a blastdb from somewhere else e.g. one of the <a href="https://ftp.ncbi.nlm.nih.gov/blast/db" rel="noreferrer">databases provided by NCBI</a> including the 16SMicrobial database. Or alternatively, when you want to double check which version of a sequence you have included in a blastdb.</p>

<fasta><blast>
How to extract fasta from a blastdb
# How to extract fasta from a blastdb

(Asked by: username_0 on 2017-06-19)

How to extract the sequence used to create a blast database. This is useful when you download a blastdb from somewhere else e.g. one of the [databases provided by NCBI](https://ftp.ncbi.nlm.nih.gov/blast/db) including the 16SMicrobial database. Or alternatively, when you want to double check which version of a sequence you have included in a blastdb.

**Tags:** fasta, blast

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## 1 answers

### Answer by username_0 on 2017-06-19. Score: 9 | Accepted answer

You can extract fasta sequence from a blastdb constructed from a fasta file using blastdbcmd which should be installed when you install blast/makeblastdb.
blastdbcmd -entry all -db  -out 

If you had a database called my_database which contained the files:

my_database.nhr 
my_database.nsq 
my_database.nin

and you wanted your fasta output file to be called reference.fasta you would run the following:
blastdbcmd -entry all -db my_database -out reference.fasta


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