This would work:
$ esearch -db protein -query "NP_001026105" | elink -target gene | esummary | xtract -pattern DocumentSummary -element Id
420087
For a lot of them you would do:
$ cat file.txt | epost -db protein -format acc | elink -target gene | esummary | xtract -pattern DocumentSummary -element Id
You should stay away from the gi numbers since they are now deprecated for end-user use.
Thank you for the help! Another question in this thread. Is there a way to get the gene descriptions (the functional role of each gene) for each entry? Something like for refseq ID: "NP_001026015.1", corresponding to gene symbol "AAR2", the description returned is "AAR2 splicing factor homolog [Source:NCBI gene;Acc:419118]"
I also worried that this command may take too long to run and terminal may time out with too many entries (currently around ~1500). Is this a legitimate concern?
$ esearch -db protein -query "NP_001026015" | elink -target gene | esummary | xtract -pattern DocumentSummary -element Name,Description
AAR2 AAR2 splicing factor homolog
Sign up for and use NCBI API key as described here. That should allow you to go through your list.
Thanks! How would I run this for a file with multiple ref sequences? I feel that it will be similar to your reply above using epost, but am not certain how to implement this.
I just created the API key. However, how do I use the API with these calls, as the documentation is a little confusing.
You can export a variable in the terminal you are doing these searches in by export NCBI_API_KEY='your_key_string'. You can also add this to your shell initialization file so it is exported when you log in.
$ cat file.txt | epost -db protein -format acc | elink -target gene | esummary | xtract -pattern DocumentSummary -element Name,Description
for line in $(cat accession_file); do printf ${line}"\t"; esearch -db protein -query $line | elink -target gene | esummary | xtract -pattern DocumentSummary -element Name,Description; done
NP_001026015 AAR2 AAR2 splicing factor homolog
NP_001026025 TTPAL alpha tocopherol transfer protein like
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Hello tom5!
You have already received answers for this in your last question :
We have closed your question to allow us to keep similar content in the same thread.
If you disagree with this please tell us why in a reply below. We'll be happy to talk about it.
Cheers!
Hi, I apologize for the similar question. However, my previous question dealt with converting protein refSeq IDs to Ensembl or Entrez gene accessions. I am now trying to convert from protein refSeq ID to Entrez gene ID. I know these are very similar tasks but I am not familiar enough with Entrez Direct to generalize the previous reply to this task.
Answer in: C: Bioinformatics: Converting Protein Refseq ID to Entrez Gene Accession will work. If it does not then can you post a couple of examples.
Yes, as an example, I want to convert the refseq ID 'NP_001026105.1' to the corresponding entrez gene ID: 420087. Is there a way to do so? My file has 1000+ refseq IDs (one per line) and I want to convert them to corresponding gene IDs. I'm sorry if you have already explained it.