Question

HIV : gtf or gff annotation

1

Entering edit mode

11.3 years ago

Nicolas Rosewick 11k

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

gtf annotation hiv gff • 11k views

ADD COMMENT • link updated 3 hours ago by Ales ▴ 50 • written 11.3 years ago by Nicolas Rosewick 11k

Ram · Answer 1 · 2014-11-06

5

Entering edit mode

10.9 years ago

Cliff Beall ▴ 480

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.

ADD COMMENT • link updated 3.9 years ago by Ram 45k • written 10.9 years ago by Cliff Beall ▴ 480

0

Entering edit mode

WOW! Great!

I did not know that there is HIV gtf available

ADD REPLY • link updated 3.9 years ago by Ram 45k • written 10.9 years ago by Manvendra Singh ★ 2.2k

0

Entering edit mode

Could you maybe please update the link? Or where I have to search?

ADD REPLY • link 7.3 years ago by caggtaagtat ★ 1.9k

0

Entering edit mode

the link is not working anymore

ADD REPLY • link 5.5 years ago by xiaoleiusc ▴ 140

score 1 · Answer 2 · 2025-09-08

1

Entering edit mode

22 days ago

Ales ▴ 50

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).

ADD COMMENT • link 22 days ago by Ales ▴ 50

0

Entering edit mode

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?

ADD REPLY • link 22 days ago by xiaoleiusc ▴ 140

1

Entering edit mode

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.

ADD REPLY • link 3 hours ago by Ales ▴ 50

Ram · Answer 3 · 2014-11-05

0

Entering edit mode

10.9 years ago

Denise CS ★ 5.2k

The only thing I got was the FASTA from ENA.

ADD COMMENT • link updated 3.9 years ago by Ram 45k • written 10.9 years ago by Denise CS ★ 5.2k

Ram · Answer 4 · 2014-11-05

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