Question: convert protein accession number to description
0
gravatar for Learner
6 months ago by
Learner 160
Learner 160 wrote:

I am wondering if anyone knows how to convert protein accession number to protein description of UniProt ?

let say I have the top 10 of this list

https://www.uniprot.org/uniprot/?query=human&sort=score

Q9H9K5
Q53XC5
P31689
P08246
P10144
P63244
P25685
Q6P2E9
O60271
Q9UBS4
gene • 272 views
ADD COMMENTlink modified 6 months ago by genomax70k • written 6 months ago by Learner 160

Could you describe what exactly you mean by "description"

ADD REPLYlink written 6 months ago by me690
0
gravatar for genomax
6 months ago by
genomax70k
United States
genomax70k wrote:

With EntrezDirect:

$ esearch -db protein -query "Q9H9K5" | esummary | xtract -pattern DocumentSummary -element Title
RecName: Full=Endogenous retroviral envelope protein HEMO; AltName: Full=Endogenous retrovirus group MER34 member 1 Env polyprotein; AltName: Full=HERV-MER_4q12 provirus ancestral Env polyprotein; AltName: Full=Human endogenous MER34 (medium-reiteration-frequency-family-34) open reading frame; AltName: Full=Human endogenous MER34 ORF; Short=HEMO; Contains: RecName: Full=Endogenous retroviral envelope protein HEMO, secreted form; AltName: Full=Endogenous retroviral envelope protein HEMO, 48 kDa form; Flags: Precursor

For a file containing accession numbers (one per line):

$ epost -db protein -input acc | esummary -db protein | xtract -pattern DocumentSummary -element Caption,Title
ADD COMMENTlink modified 6 months ago • written 6 months ago by genomax70k

This will fail in a large number of cases as the NCBI does not have all UniProt accessions.

ADD REPLYlink written 6 months ago by me690

I think OP is only looking at human genes so I assume they should all be present.

OP could always use the UniProt ID mapping service and download any column they want from the results table.

ADD REPLYlink modified 6 months ago • written 6 months ago by genomax70k
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