Hi,
I have a list of virus names; here's the top of the list:
Honey bee slow paralysis virus
Theilovirus
Taura syndrome virus
Triatoma virus
Equine rhinitis B virus
Drosophila C virus
Black queen cell virus
Sacbrood virus
...
I'd like to organise these by their main host type: plant/invertebrate/vertebrate viruses (which I know is a probably a very rough organisation). I was wondering if there was a good way of going about this, that didn't involve me googling each virus individually. I have 148 in my list, and would like to be able to automatically add more should I be given them. At the moment I'm doing a pretty hacky google based enrichment study, which isn't working that well!
Are there any dedicated databases that would help?
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written
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Mike Dewar
Don't know if this would answer your question but you can download an excel file with a master list of virus and theirs hosts here. Another option might be to use the taxonomy entries on NCBI to get the virus and their host, maybe searching for keywords in their names.
I think what I need to do is classify the hosts - rather than "this virus is popular amongst strawberries", I'd like to know "this virus is a plant virus" - or maybe more accurately "this virus started off as a plant virus"
There's a universal virus database that contains a lot of information, including known hosts for viruses. You'd have to look though, which of their many pages and lists allows you to extract this information most easily.
You can have a look at the RNA Virus database [?]At the bottom of the web page there is the possibility to browse the listing either by family or genus. Or you can display the complete listing.[?] [?]You can may be get what you want by parsing the html code of the webpage[?]
Can I infer a super-set of host types, like plant, vertebrate, invertebrate, (rather than strawberry, bee, drosophila, pig...) from the genus of the virus? A cursory look says no but then I don't have any ability to properly parse the Latin...
For those viruses with proteins in the UniProt database, there is a "Virus host" field in the "Names and origin" section. See this page for some details.
UniProt has a pretty good taxonomy hierarchy; you could probably start from somewhere like this information, fetch all protein records for viruses and extract host names.
bingo! Thanks a lot.
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see also Bio.Entrez - Get virus host name using NCBI Taxonomy db