Question: HIV : gtf or gff annotation
0
gravatar for Nicolas Rosewick
4.3 years ago by
Belgium, Brussels
Nicolas Rosewick6.7k wrote:

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

hiv gff annotation gtf • 1.8k views
ADD COMMENTlink modified 3.9 years ago by Cliff Beall450 • written 4.3 years ago by Nicolas Rosewick6.7k
4
gravatar for Cliff Beall
3.9 years ago by
Cliff Beall450
Ohio
Cliff Beall450 wrote:

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 COMMENTlink written 3.9 years ago by Cliff Beall450

WOW! Great! 

I did not know that there is HIV  gtf available

ADD REPLYlink written 3.9 years ago by Manvendra Singh2.0k

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

ADD REPLYlink written 3 months ago by caggtaagtat330
0
gravatar for Denise - Open Targets
3.9 years ago by
UK, Hinxton, EMBL-EBI
Denise - Open Targets4.7k wrote:

The only thing I got was the FASTA from ENA.

ADD COMMENTlink written 3.9 years ago by Denise - Open Targets4.7k
0
gravatar for Manvendra Singh
3.9 years ago by
Manvendra Singh2.0k
Berlin, Germany
Manvendra Singh2.0k wrote:

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,

allign them to see and make co-ordinates of each proteins and consequently edit it is in GTF format

ADD COMMENTlink written 3.9 years ago by Manvendra Singh2.0k
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