Question

HIV : gtf or gff annotation

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9.8 years ago

Nicolas Rosewick 10k

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 • 4.4k views

ADD COMMENT • link updated 2.5 years ago by Ram 43k • written 9.8 years ago by Nicolas Rosewick 10k

Ram · Answer 1 · 2014-11-06

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9.5 years ago

Cliff Beall ▴ 470

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 2.5 years ago by Ram 43k • written 9.5 years ago by Cliff Beall ▴ 470

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WOW! Great!

I did not know that there is HIV gtf available

ADD REPLY • link updated 2.5 years ago by Ram 43k • written 9.5 years ago by Manvendra Singh ★ 2.2k

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

ADD REPLY • link 5.8 years ago by caggtaagtat ★ 1.9k

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the link is not working anymore

ADD REPLY • link 4.1 years ago by xiaoleiusc ▴ 140

Ram · Answer 2 · 2014-11-05

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9.5 years ago

Denise CS ★ 5.2k

The only thing I got was the FASTA from ENA.

ADD COMMENT • link updated 2.5 years ago by Ram 43k • written 9.5 years ago by Denise CS ★ 5.2k

Ram · Answer 3 · 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