HIV virus - GTF annonation

Question

[maxdlf12]

Hello, I'm working on a project of detecting RNA fragments of HIV virus in blood. I'm hoping to find GTF annotation of HIV virus to use in stringtie, but it seems quite difficult to find. Does anybody happen to have a file?

There was another post that had a link to it but unfortunately it seems to have expired.

Acquiring this file would really ease the process of my project and I'm hoping someone might have one here.

Thanks.

Answer 1

[Shred]

Here you go: https://www.ncbi.nlm.nih.gov/genome/10319

Genome annotation / GFF

[maxdlf12]

Ah, I guess this is all i can get. Thanks for your help :)

Answer 2

[Ales]

For anyone stumbling on this. There exists a plethora of literature detailing the splicing patterns in HIV and SIV, major and minor donor/acceptor sites, junctions, transcripts and proteins. However no standardized GTF/GFF file suitable for computational analysis was available unfortunately.

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).