text: user302: I'm looking for the exact invocation used to generate the 16SMicrobial database that you can download from here:
  https://ftp.ncbi.nlm.nih.gov/blast/db/
  I'm hoping to create the same type of blastdb with the same type of metadata with custom sequences.
  Platform isn't an issue, but let's say on ubuntu 14.04 or 16.04.
  I would like to replicate the creation of the database as closely as possible. 
   The most important feature is the taxonomic information as can be seen here:
  
  The databases on the FTP site contain taxonomic information for each
    sequence, include the identifier indices for lookups, and can be up to
    four times smaller than the FASTA. The original FASTA can be generated
    from the BLAST database using blastdbcmd
  
  Creation of a blastdb using makeblastdb from a set of a fasta sequences is not an issue and can be achieved via:
  makeblastdb -in <your_file.fasta> -dbtype nucl -out <database_name>
  
  My question is specifically about the invocation NCBI uses to add the metadata that is present in the NCBI's 16SMicrobial blast database as I am keen to make sure I have replicated the process as closely as possible.
  
  user941: Running blastdbcmd -db foo -info provides a little information but I haven't seen anything which will report exactly how a blastdb was created.
  A blastdb readme suggests that only the parse_seqids option has been added to the standard parameters.
  
  For those from NCBI, the following makeblastdb commands are recommended:
  
  For nucleotide fasta file:   makeblastdb -in input_db -dbtype nucl -parse_seqids
  For protein fasta file:      makeblastdb -in input_db -dbtype prot -parse_seqids
  
  
  The -parse_seqids requires NCBI fasta headers in the correct format (spec can be found here).
  
original_text: 302: <p>I'm looking for the exact invocation used to generate the 16SMicrobial database that you can download from here:</p>
  
  <p><a href="https://ftp.ncbi.nlm.nih.gov/blast/db/" rel="nofollow noreferrer">https://ftp.ncbi.nlm.nih.gov/blast/db/</a></p>
  
  <p>I'm hoping to create the same type of blastdb with the same type of metadata with custom sequences.</p>
  
  <p>Platform isn't an issue, but let's say on ubuntu 14.04 or 16.04.</p>
  
  <p>I would like to replicate the creation of the database as closely as possible. 
   The most important feature is the taxonomic information as can be seen <a href="https://www.ncbi.nlm.nih.gov/books/NBK279688/" rel="nofollow noreferrer">here</a>:</p>
  
  <blockquote>
    <p>The databases on the FTP site contain taxonomic information for each
    sequence, include the identifier indices for lookups, and can be up to
    four times smaller than the FASTA. The original FASTA can be generated
    from the BLAST database using blastdbcmd</p>
  </blockquote>
  
  <p>Creation of a blastdb using makeblastdb from a set of a fasta sequences is not an issue and can be achieved via:</p>
  
  <pre><code>makeblastdb -in &lt;your_file.fasta&gt; -dbtype nucl -out &lt;database_name&gt;
  </code></pre>
  
  <p>My question is specifically about the invocation NCBI uses to add the metadata that is present in the NCBI's 16SMicrobial blast database as I am keen to make sure I have replicated the process as closely as possible.</p>
   941: <p>Running <code>blastdbcmd -db foo -info</code> provides a little information but I haven't seen anything which will report exactly how a blastdb was created.</p>
  <p>A <a href="https://ftp.ncbi.nlm.nih.gov/blast/documents/blastdb.html" rel="nofollow noreferrer">blastdb readme</a> suggests that only the <code>parse_seqids</code> option has been added to the standard parameters.</p>
  <blockquote>
  <p>For those from NCBI, the following makeblastdb commands are recommended:</p>
  <ul>
  <li>For nucleotide fasta file:   makeblastdb -in input_db -dbtype nucl -parse_seqids</li>
  <li>For protein fasta file:      makeblastdb -in input_db -dbtype prot -parse_seqids</li>
  </ul>
  </blockquote>
  <p>The <code>-parse_seqids</code> requires NCBI fasta headers in the correct format (spec can be found <a href="http://ncbi.github.io/cxx-toolkit/pages/ch_demo#ch_demo.id1_fetch.html_ref_fasta" rel="nofollow noreferrer">here</a>).</p>
  