Question: HIV : gtf or gff annotation
0
gravatar for Nicolas Rosewick
3.4 years ago by
Belgium, Brussels, Université Libre de Bruxelles / Université de Liège
Nicolas Rosewick5.7k 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 • 1.3k views
ADD COMMENTlink modified 3.0 years ago by Cliff Beall440 • written 3.4 years ago by Nicolas Rosewick5.7k
4
gravatar for Cliff Beall
3.0 years ago by
Cliff Beall440
Ohio
Cliff Beall440 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 3.0 years ago by Cliff Beall440

WOW! Great! 

I did not know that there is HIV  gtf available

ADD REPLYlink written 3.0 years ago by Manvendra Singh1.9k
0
gravatar for Denise - Open Targets
3.0 years ago by
UK, Hinxton, EMBL-EBI
Denise - Open Targets4.1k wrote:

The only thing I got was the FASTA from ENA.

ADD COMMENTlink written 3.0 years ago by Denise - Open Targets4.1k
0
gravatar for Manvendra Singh
3.0 years ago by
Manvendra Singh1.9k
Berlin, Germany
Manvendra Singh1.9k 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 3.0 years ago by Manvendra Singh1.9k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1459 users visited in the last hour