This is a test version of Biostars. For the public version, visit https://www.biostars.org.
How to check if a list of protein ID's are present in NCBI protein database?

I have a list of protein IDs. An example list is as follows. How can I use esearch esearch -db protein -query <listids> in protein database to identify those that are not present in the protein database?

ADK95960.1
PQL24628.1
AVM48340.1
ADK95748.1
EFX40722.1
AKU69507.1
AVM47886.1
ADK96247.1
NOT9000.1
esearch protein database ncbi
• 1,595 views • link
written by mrj • mrj

1 answer

You can do it with esummary:

If your accesions are in file called ids then the following will fetch the json format for each:

URL='https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=protein\&format=json\&id='

cat ids | parallel -j 1 curl -s  ${URL}{} > results.txt

where the results.txt file will contain lines such as:

{"header":{"type":"esummary","version":"0.3"},"error":"Invalid uid NOT9000.1 at position=0","result":{"uids":[]}}

for the invalid entries.

• 0 views • link
written by Istvan Albert Istvan Albert

Thank you. It worked

• 0 views • link
written by mrj • mrj

Log in to answer this question.

More posts like this