Retrieving a list of protein names in a search result

Question

[Willem]

I'm new here, so if duplicates are around, feel free to redirect.

Imagine that you have searched all proteins of a specific virus and that you want to have a list of all the possible protein name entries of that virus. That way you can see which search terms there are to sort the collection of sequences for the proteins of that virus (since the same type of protein sometimes has a different name in uniprot).

I want to give some code that I tried, but in the end I wouldn't know how to even start. I'm pretty new and so far only know a bit of python.

Thanks!

[me]

Could you let us know what your starting data is. taxid? virus name? dna sequences? uniprotkb ids or acs?

[Willem]

Well, the only thing I have is the virus taxonomy ID.

Answer 1

[Elisabeth Gasteiger]

If you have a tax_id, you can use URLs of the type (for tax_id 79692, Human respiratory syncytial virus B)

http://www.uniprot.org/uniprot/?query=taxonomy:79692&format=tab&columns=id,entry%20name,protein%20names

If you don't have the tax_id but an organism name, enter http://www.uniprot.org/taxonomy to find your virus and the corresponding tax_id.

[Willem]

Thank you, I'll try this method.

Answer 2

[5heikki]

If you have protein GI, then you can use Entrez Direct as such (perhaps you are interested in only some of the "elements" listed below):

epost -db protein -id 2887457 | elink -target gene | efetch -format docsum | xtract -element Name -element Description -element OtherAliases -element OtherDesignations -element NomenclatureSymbol -element NomenclatureName
DHH    desert hedgehog    GDXYM, HHG-3, SRXY7    desert hedgehog homolog|mutant desert hedgehog    DHH    desert hedgehog

[Willem]

I don't think I have the protein GI, or rather I don't know how to retrieve a list of all GI's of the proteins I'm filtering. Are there any links for more information on how to use GI's and Entrez together with python?