Viral sequences in hg19

[Liy]

Dear all,

I'm trying to obtain viral sequence loci in the human genome. Can anyone suggest an easy way to do this?

I found several endogenous retrovirus sites in papers, but i want to analyze other viruses also.

I have downloaded a virus database that contains 32102 viral genomes as fasta format. May I use blast or align to the hg19? Is there a catalog of these sites?

I would appreciate your help.

Regards,
Laszlo

[dpryan]

It's probably faster to just use the repeatmasker output for hg19. It'll have a lot of the integrated viral species. You can download that from UCSC.

[Liy]

Thank you! Ill check this out!