Question

Mapping Between GenBank ID's and Uniprot

0

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georgii.vdovin • 0

@2289c15f

Last seen 5 days 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 • 1.1k views

ADD COMMENT • link written 5 months ago by georgii.vdovin • 0

0

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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

ADD REPLY • link 5 months ago Marcel Ramos 700

0

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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.

ADD REPLY • link 5 months ago James W. MacDonald 67k

score 3 · Accepted Answer · 2024-07-05

3

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James W. MacDonald 67k

@james-w-macdonald-5106

Last seen 18 hours ago

United States

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

ADD COMMENT • link 5 months ago James W. MacDonald 67k

1

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Ugh, here's the link

https://www.uniprot.org/id-mapping/uniprotkb/dd08aa16774d98ef087dc3bd708582012bba49e2/overview?fields=accession%2Creviewed%2Cid%2Cprotein_name%2Cgene_names%2Corganism_name%2Clength

ADD REPLY • link 5 months ago James W. MacDonald 67k

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