Bioinformatics Asked by Ehsan Salehabadi on July 3, 2021
Are there any databases or tools that contain a list of all RefSeq protein IDs for the interest organism/microorganism, e.g. get a specific microorganism name and return all RefSeq Protein IDs that have been identified?
How about using RefSeq itself? Say, you are interested in all E. coli proteins, you can use the query "Escherichia coli"[Organism] AND RefSeq[Filter] here.
If you know the Taxonomy identifier for the specific organism of interest to you, it can also be used. For example, if you are interested in only "Escherichia coli str. K-12 substr. DH10B", you can use the taxonomy identifier 316385 (obtained from here) in the query txid316385[Organism] AND RefSeq[Filter].
To extract a list of accessions and save them to a file on disk, use the "Send To" menu at the top right corner, choose "File" as destination followed by "Accession List" as the format and download the file.
Answered by vkkodali on July 3, 2021
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