text: user2880: I am trying to use HIVdb(https://hivdb.stanford.edu/hivdb/by-sequences/) program. I have a HIV protease which I want to test with most commonly used PIs. But when I entered it in fasta sequence format to the HIVdb, it give me error code saying 
  
  Critical: There were no Protease, Reverse Transcriptase, or Integrase genes found, refuse to process.
  
  For example, if I download FASTA sequence of 1HPV from PDB and paste it in HIVdb input sequence window as below,
  PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLVGPT
  PVNIIGRNLLTQIGCTLNF
  
  I get the error code. Any suggestion on how to input sequences in HIVdb?
  (Note: I am new to this subject)
  
  user298: The HIVdb page states the following in the second paragraph (emphasis mine):
  
  Sequences can be entered as plain text if just one sequence is entered. Sequences must be entered using the FASTA format if multiple sequences are entered. Sequences can be pasted in the text box or uploaded using the File Upload option. The upper limit is currently 1000 sequences containing 3000 nucleotides per sequence.
  
  The sequence in your question is a protein, so it consists of amino acids, not nucleotides. So, if you instead give a nucleotide sequence, for example this one:
  >KX692212.1 HIV-1 isolate CH47 from Switzerland pol protein (pol) and gag protein (gag) genes, partial cds
  CCTCAGATCACTCTTTGGCAACGACCCCTCGTCACAATAAAGATAGGGGGGCAACTAAAGGAAGCTCTAT
  TAGATACAGGAGCAGATGATACAGTATTAGAAGAAATGAGTTTGCCAGGAAGATGGAAACCAAAAATGAT
  AGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGATCAGATACTCATAGAAATCTGTGGACATAAA
  GCTATAGGTACAGTATTAGTAGGACCTACACCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGATTG
  GTTGCACTTTAAATTTT
  
  The program will work as expected:
  
  
  For future reference, I found the KX692212 sequence above by taking your protein sequence and running a tBLASTn analysis against HIV sequences in NCBI's nr database. That was the first hit.
  
original_text: 2880: <p>I am trying to use HIVdb(<a href="https://hivdb.stanford.edu/hivdb/by-sequences/" rel="nofollow noreferrer">https://hivdb.stanford.edu/hivdb/by-sequences/</a>) program. I have a HIV protease which I want to test with most commonly used PIs. But when I entered it in fasta sequence format to the HIVdb, it give me error code saying </p>
  
  <blockquote>
    <p>Critical: There were no Protease, Reverse Transcriptase, or Integrase genes found, refuse to process.</p>
  </blockquote>
  
  <p>For example, if I download FASTA sequence of 1HPV from PDB and paste it in HIVdb input sequence window as below,</p>
  
  <pre><code>PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLVGPT
  PVNIIGRNLLTQIGCTLNF
  </code></pre>
  
  <p>I get the error code. Any suggestion on how to input sequences in HIVdb?
  (Note: I am new to this subject)</p>
   298: <p>The HIVdb page states the following in the second paragraph (emphasis mine):</p>
  
  <blockquote>
    <p>Sequences can be entered as plain text if just one sequence is entered. Sequences must be entered using the FASTA format if multiple sequences are entered. Sequences can be pasted in the text box or uploaded using the File Upload option. The upper limit is currently 1000 sequences containing 3000 <strong>nucleotides</strong> per sequence.</p>
  </blockquote>
  
  <p>The sequence in your question is a protein, so it consists of amino acids, not nucleotides. So, if you instead give a nucleotide sequence, for example <a href="https://www.ncbi.nlm.nih.gov/nuccore/KX692212.1?report=genbank" rel="nofollow noreferrer">this one</a>:</p>
  
  <pre><code>&gt;KX692212.1 HIV-1 isolate CH47 from Switzerland pol protein (pol) and gag protein (gag) genes, partial cds
  CCTCAGATCACTCTTTGGCAACGACCCCTCGTCACAATAAAGATAGGGGGGCAACTAAAGGAAGCTCTAT
  TAGATACAGGAGCAGATGATACAGTATTAGAAGAAATGAGTTTGCCAGGAAGATGGAAACCAAAAATGAT
  AGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGATCAGATACTCATAGAAATCTGTGGACATAAA
  GCTATAGGTACAGTATTAGTAGGACCTACACCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGATTG
  GTTGCACTTTAAATTTT
  </code></pre>
  
  <p>The program will work as expected:</p>
  
  <p><a href="https://i.stack.imgur.com/rUzD4.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/rUzD4.png" alt="HIVdb output"></a></p>
  
  <hr>
  
  <p>For future reference, I found the KX692212 sequence above by taking your protein sequence and running a <a href="https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=Translations&amp;PROGRAM=tblastn&amp;PAGE_TYPE=BlastSearch&amp;BLAST_SPEC=" rel="nofollow noreferrer">tBLASTn</a> analysis against HIV sequences in NCBI's <code>nr</code> database. That was the first hit.</p>
  