Answers.Body: <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.sstatic.net/rUzD4.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-05-31T15:35:32.877Z
Answers.Text: Yes, It worked. I didn't notice "nucleotides" emphasis.
Answers.UserDisplayName: Vajira
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-05-31T15:04:07.890Z
Answers.LastActivityDate: 2018-05-31T15:04:07.890Z
Answers.UserDisplayName: terdon
Body: <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>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-05-31T14:41:23.053Z
Comments.Text: I am not familiar with this database or tool, so this is just a guess. Did you try to input DNA or nucleotide sequence?
Comments.UserDisplayName: benn
Tags: <fasta>
Title: HIVdb program and FASTA sequence input
ThreadText: # HIVdb program and FASTA sequence input
  
  (Asked by: username_0 on 2018-05-31)
  
  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)
  
  **Tags:** fasta
  
  > **Comments:**
  > **username_1**: I am not familiar with this database or tool, so this is just a guess. Did you try to input DNA or nucleotide sequence?  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2018-05-31. Score: 1 | Accepted answer
  
  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](https://www.ncbi.nlm.nih.gov/nuccore/KX692212.1?report=genbank):
  
  ```
  >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:
  
  [![HIVdb output](https://i.sstatic.net/rUzD4.png)](https://i.sstatic.net/rUzD4.png)
  
  ---
  
  For future reference, I found the KX692212 sequence above by taking your protein sequence and running a [tBLASTn](https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=Translations&PROGRAM=tblastn&PAGE_TYPE=BlastSearch&BLAST_SPEC=) analysis against HIV sequences in NCBI's `nr` database. That was the first hit.
  
  > **Comments:**
  > **username_0**: Yes, It worked. I didn't notice "nucleotides" emphasis.  
  
  ---
  
  