Question: convert protein accession number to description
0
gravatar for Learner
16 months ago by
Learner 220
Learner 220 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 • 606 views
ADD COMMENTlink modified 16 months ago by genomax83k • written 16 months ago by Learner 220

Could you describe what exactly you mean by "description"

ADD REPLYlink written 16 months ago by me690
0
gravatar for genomax
16 months ago by
genomax83k
United States
genomax83k 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 16 months ago • written 16 months ago by genomax83k

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

ADD REPLYlink written 16 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 16 months ago • written 16 months ago by genomax83k
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