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
•
written
by
Nicolas Rosewick
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.
•
written
by
Cliff Beall
WOW! Great!
I did not know that there is HIV gtf available
•
written
by
Manvendra Singh
Could you maybe please update the link? Or where I have to search?
the link is not working anymore
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).
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?
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.
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
•
written
by
Manvendra Singh
Log in to answer this question.
