Question: ID-Mapping: EntrezProtein to UniprotKB
0
gravatar for bi_Scholar
2.5 years ago by
bi_Scholar0
bi_Scholar0 wrote:

Hello, what is the go-to way for mapping Entrez-Protein-ID to Uniprot? I usually use the Uniprot-Mappingservice but unfortunately it doesn't cover Entrez-Proteins.

Cheers

mapping uniprot entrez • 680 views
ADD COMMENTlink modified 2.5 years ago by EagleEye6.2k • written 2.5 years ago by bi_Scholar0
1

These are RefSeq/Genpept ID's or something else?

ADD REPLYlink written 2.5 years ago by genomax64k

They are Entrez-Protein-IDs, at least thats what the column in my database states.

ADD REPLYlink written 2.5 years ago by bi_Scholar0
1

Can you post a few examples? If the answer provided by @EagleEye is satisfactory then you are all set.

ADD REPLYlink modified 2.5 years ago • written 2.5 years ago by genomax64k

Here are some sample-entries:

Entrez Protein  AAF22032
Entrez Protein  BAC85338
Entrez Protein  BAE48238
Entrez Protein  BAB71206
Entrez Protein  BAC85939

In the linked post from @EagleEye , BioMart is proposed to create a mapping-file, but I can't find an option to include Entrez IDs.

ADD REPLYlink modified 2.5 years ago • written 2.5 years ago by bi_Scholar0
3

These appear to be cDNA's (that may also be translated). From the examples you posted here I was able to convert 4 out of 5 using the UniProt ID converter tool and "EMBL/GenBank/DDBJ CDS" as the "From" option. See how many you can get that way.

ADD REPLYlink written 2.5 years ago by genomax64k

Wow, thanks alot! I could map >90% of 40k IDs, which is more than enough for what I'm doing.

ADD REPLYlink written 2.5 years ago by bi_Scholar0
1
gravatar for EagleEye
2.5 years ago by
EagleEye6.2k
Sweden
EagleEye6.2k wrote:

You will find information you needed in this link. I guess you are looking for mapping Entrez ids to Uniprot Ids.

C: Reliable Database containing info for Entrez ID's and Entrez Symbols

ADD COMMENTlink modified 2.5 years ago • written 2.5 years ago by EagleEye6.2k
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