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Proteomicslab57357 / UniprotR

Retrieving Information of Proteins from Uniprot
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Cannot convert UniProtKB AC/ID to UniProtKB #8

Closed goncik closed 4 years ago

goncik commented 4 years ago

Hi,

I have a csv file with one column consist of UniProtKB AC/ID's as the following:

1433B_HUMAN 1433E_HUMAN 1433F_HUMAN 1433G_HUMAN 1433S_HUMAN 1433T_HUMAN

And I want to convert my list into UniProtKB ie, P31946, P62258, Q04917...

I tried doing this in R writing this: ConvertID(ProteinAccList = substrate$Substrate_Uniprot_ID, ID_from = "UniProtKB_AC_ID" , ID_to = 'UniProtKB')

It worked but returned an empty list:

From_UniProtKB_AC_ID To UniProtKB 1 1433B_HUMAN
2 1433E_HUMAN
3 1433F_HUMAN
4 1433G_HUMAN
5 1433S_HUMAN
6 1433T_HUMAN

I don't know if I do it wrong but I appreciate any help from your side because I have thousands of proteins to convert :)

Many thanks!

AliYoussef96 commented 4 years ago

Hi,

Uniprot DB use different names of IDs and accessions number, so in the code just pass ID_to = "ACC" instead of ID_to = "UniProtKB" and without ID_from.

library("UniprotR")
ids <- c("1433B_HUMAN",
         "1433E_HUMAN",
         "1433F_HUMAN",
         "1433G_HUMAN",
         "1433S_HUMAN",
         "1433T_HUMAN")

ConvertID(ProteinAccList = ids , ID_to = 'ACC')
  From_UniProtKB_AC_ID To ACC
1          1433B_HUMAN P31946
2          1433E_HUMAN P62258
3          1433F_HUMAN Q04917
4          1433G_HUMAN P61981
5          1433S_HUMAN P31947
6          1433T_HUMAN P27348