HIV : gtf or gff annotation

Question

[Nicolas Rosewick]

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

Answer 1

[Cliff Beall]

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.

[Manvendra Singh]

WOW! Great!

I did not know that there is HIV gtf available

[caggtaagtat]

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

[xiaoleiusc]

the link is not working anymore

Answer 2

[Ales]

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).

[xiaoleiusc]

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?

Answer 3

[Denise CS]

The only thing I got was the FASTA from ENA.

Answer 4

[Manvendra Singh]

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