Entering edit mode
6.2 years ago
caggtaagtat
★
1.9k
Hi,
for my comparison of viral genomes, I would like to download genomes of retroviruses, which infect humans. Unfortunatly, I do not find any genomes of retroviruses in any databases.
I would be interested in the final viral DNA sequence after integration in the human genome.
Until now, I only found the HERV database, which is limited on endogenous retroviruses which can already be found in the human genome.
Every advise is appreciated :)
I only found reference genomes, which had to be collected by copy and paste.
For other viurs families, there are giant databases of viral genome subtypes, which can be downloaded, like here: https://www.viprbrc.org/brc/home.spg?decorator=vipr
You asked for retroviruses so @Jean-Karim provided a page specific for those (they are not all human). RefSeq has all validated viral genomes. Are your needs not covered between the links here?
I will save the link you send, but right now I'm not interested in the reference sequence of for example HIV1 but in the sequnence of different subtypes of HIV1, like it is for other virus families in the database I mentioned.
You may have already seen the database at LANL then.
No, but since the number of different retroviruses which affect humans is very low and my approach is very broad for now, I will just use HIV as a representative for retroviruses. Thanks :)
From the NCBI retroviridae page, use the "retrieve sequences" menu in the upper right and select "RefSeq plus neighbor nucleotides", which will send you to this link: https://www.ncbi.nlm.nih.gov/nuccore?term=Retroviridae[Organism]+NOT+cellular+organisms[ORGN]+NOT+wgs[PROP]+NOT+AC_000001:AC_999999[pacc]+NOT+gbdiv+syn[prop]+AND+(srcdb_refseq[PROP]+OR+nuccore+genome+samespecies[Filter])
You can further refine that query if you'd like, and download the set using the "Send to" menu