text: user302: 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 including the 16SMicrobial database. Or alternatively, when you want to double check which version of a sequence you have included in a blastdb.
  
  user302: 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 <database label> -out <outfile>
  
  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
  
  
original_text: 302: <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>
   302: <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>
  