When I searched HIV on NCBI gene bank, I found 2 results from 1997: http://www.ncbi.nlm.nih.gov/genome/?term=HIV. HIV can change every day, so I think the sequence from 1997 is not useful. Is it?

  • $\begingroup$ Please give some more information on what you are trying to do. $\endgroup$
    – terdon
    Commented Jul 7, 2013 at 16:44
  • $\begingroup$ I'm trying to design a primer to detect HIV so i need an up to date sequence of HIV. But the one in NCBI Genebank is from 1997 and i think it's not useful anymore. $\endgroup$ Commented Jul 8, 2013 at 0:56
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    $\begingroup$ My impression from your questions is that you're doing DIY biology and are not in a corporate or academic lab. I'd very strongly suggest you to avoid doing anything with potentially HIV-infected material, handling this requires at least a biosafety level 2 laboratory. Handling HIV without proper precautions and permits could result in infecting yourself and potentially a lot of legal trouble or even criminal charges. $\endgroup$ Commented Jul 8, 2013 at 6:39
  • $\begingroup$ Hello, thank you so much for your advised. However, i just give an example. May be i will try on other virus/bacterial , should i using the sequence from NCBI to design primer when it's not up to date ? Any other database better than NCBI ? $\endgroup$ Commented Jul 8, 2013 at 6:43
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    $\begingroup$ @ĐứcUltraSoft you can look at highly conserved sequences in viral/bacterial genome. But as told in the other comment, don't work with pathogenic microbes. $\endgroup$
    Commented Jul 8, 2013 at 9:25

1 Answer 1


Any other database better than NCBI ?

A lot of people overlook some sub-databases inside NCBI and search the main nucleotide database only.

If You never tried it, you can blast the HIV sequence which You have found, against other databases. On the ncbi blast webpage, just choose the options other than nucleotide collection (nr/nt). I tend to find new sequences in Expressed sequence tags (EST), Genomic survey sequences (GSS) or Whole genome shotgun contigs (WGS). Some of these databases cover unfinished sequencing project and should be a source of new data.

(I am a plant person, not virus person, so maybe you will find out, that different databases are worth searching for you. Or you will find it a waste of time.)

BTW, now some time had passed since your question. How did you solve Your HIV sequence problem ?


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