Mapping Between GenBank ID's and Uniprot
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0
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@2289c15f
Last seen 9 hours ago
Germany

Hello, I need to map GenBank protein ID's to corresponding Uniprot ID's from non-model organisms (e.g. ACF95883.1 = https://www.uniprot.org/uniprotkb/B5ATG2/entry = SOX9). I am struggling to find tools to do so, could anyone please help?

# This failed

up <- UniProt.ws()


result <- mapUniProt(
  from = "EMBL-GenBank-DDBJ",
  to = "UniProtKB",
  query = c("ACF95883.1") 
)

print(result)

() waiting for query completion.......... 00:00:02 Warning: IDs not mapped: ACF95883.1

UniProt.ws AnnotationDbi • 332 views
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Entering edit mode

Hi georgii.vdovin

To verify, I tried the same query at

https://www.uniprot.org/id-mapping/uniprotkb/3e1ca27409d1622678b03b2dd1e79878fd431a67/input-parameters

and did not get a result. Perhaps the ID is not in the database?

Note. See also: https://getentry.ddbj.nig.ac.jp/getentry/na/ACF95883.1/?filetype=html

Best regards,

Marcel

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Entering edit mode

It is in the database, but it's a TrEMBL ID, and it's not clear to me that you can map using the API.

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@james-w-macdonald-5106
Last seen 1 hour ago
United States

The input should be 'EMBL-GenBank-DDBJ_CDS", as that is a GenBank ID.

1
Entering edit mode

Also,

> result <- mapUniProt(
  from = "EMBL-GenBank-DDBJ_CDS",
  to = "UniProtKB",
  query = c("ACF95883.1") 
)
> result
        From  Entry   Entry.Name   Reviewed Protein.names Gene.Names                                Organism
1 ACF95883.1 B5ATG2 B5ATG2_PLEWA unreviewed          SOX9         NA Pleurodeles waltl (Iberian ribbed newt)
  Length
1    479
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Thanks a lot!

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