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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)

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  • $\begingroup$ I am not familiar with this database or tool, so this is just a guess. Did you try to input DNA or nucleotide sequence? $\endgroup$ – benn May 31 '18 at 14:41
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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:

HIVdb output


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.

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  • $\begingroup$ Yes, It worked. I didn't notice "nucleotides" emphasis. $\endgroup$ – Vajira May 31 '18 at 15:35

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