WOW! Great!
I did not know that there is HIV gtf available
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HIV : gtf or gff annotation
Hi,
I'm looking for a gtf of a gff for HIV genome (and its associated fasta sequence).
I'm not into active HIV research so I ask biostars people if they can help me a little bit ;)
Thanks
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4 answers
ftp://ftp.ncbi.nlm.nih.gov/genomes/Viruses/Human_immunodeficiency_virus_1_uid15476/NC_001802.gff
By the way, Manu, there are quite a few other genes in there as well: tat, rev and all that good stuff.
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For anyone stumbling on this. We have recently completed reference-grade annotation for several thousand HIV-1 genomes including the main HXB2 (K03455.1) reference genome: https://ccb.jhu.edu/HIV_Atlas/. Each annotation features full set of US, PS and FS messages along with protein assignment and major donor and acceptor sites. The annotations are provided in GTF and GFF formats, you can browse them directly on the web interface via integrated JBrowse2 and use them with any transcriptomic utilities you would use for human or other genomes (assembly, quantification, gene/tx expression, etc).
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Thank you for all your efforts! This is an important achievement. Could you please provide a citation link so we can properly reference your work?
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Thank you for your response! We have just posted the full preprint to BioRxiv (https://www.biorxiv.org/content/10.1101/2025.09.24.675449v1). The manuscript covers all aspects of the work including construction, some interesting facts that came up during this work and numerous demonstrations of its utility for various research tasks. Very excited for people to use it and am very welcoming to discuss feedback and requests!
P.S.: Right before the manuscript was posted, I manually added NL4-3 and 89.6 isolate sequences and annotations to the resource, which were missing at the time of my original post.
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I downloaded NL4-3 and found only AF324493.2.fasta, AF324493.2.gff.gz, and AF324493.2.fasta.fai; I did not find a GTF file. Is this normal?
In addition, the NL4-3 FASTA sequence is approximately 14 kb, whereas the HIV-1 genome is only about 10 kb. It therefore appears that this sequence corresponds to a plasmid containing the HIV-1 sequence, rather than to the HIV-1 viral genome alone.
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The GTF annotation and the analysis of HIV-1 splice-site conservation do not include the A4d splice acceptor. However, A4d is used by NL4-3 and appears to be less conserved across HIV-1 strains (https://journals.asm.org/doi/10.1128/jvi.02515-16?url_ver=Z39.88-2003&rfr_id=ori%3Arid%3Acrossref.org&rfr_dat=cr_pub++0pubmed)
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I don't think that there is HIV gtf
HIV is Retro-Virus.
I think
Full length HIV has the usual retro-viral structure as:
5'LTR-GAG-POL-PRO-RT-ENV-3'LTR
they also have some accessory coding proteins
best way is to fetch fasta sequence of full-length HIV, and viral proteins,
Align them to see and make co-ordinates of each proteins and consequently edit it is in GTF format
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