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elink:tldr:5b001
elink: Search pubmed then find related sequences.
$ esearch -db pubmed -query "${selective serotonin reuptake inhibitor}" | elink -target nuccore
try on your machine
The command you mentioned consists of two parts, separated by the pipe symbol "|".
-
esearch -db pubmed -query "${selective serotonin reuptake inhibitor}":
- This part uses the "esearch" command-line tool.
- It is used to perform a search in the PubMed database ("pubmed" is specified as the "-db" option).
- The search query is "${selective serotonin reuptake inhibitor}". The phrase is wrapped in "${...}" to indicate that it is a variable name.
- The specific query term is not provided in this command; it should be replaced with the desired term by the user. For example, if the desired term is "fluoxetine", the command will be "esearch -db pubmed -query "fluoxetine"".
- The command will search for papers related to the specified query term in the PubMed database. It will provide a list of matching PubMed IDs (PMIDs) as output.
-
elink -target nuccore:
- This part uses the "elink" command-line tool.
- It is used to query related links in NCBI databases based on the provided list of PMIDs.
- The "-target nuccore" option specifies that the desired target database is "nuccore", which contains nucleotide sequences.
- The output from the "esearch" command (list of PMIDs) is passed as input to the "elink" command.
- The "elink" command will retrieve the related nucleotide objects/sequences from the "nuccore" database, associated with the papers retrieved in the previous step.
In summary, the combined command allows you to search PubMed for papers related to a specific term (such as a selective serotonin reuptake inhibitor), and then retrieve the related nucleotide sequences from the "nuccore" database for those papers.
This explanation was created by an AI. In most cases those are correct. But please always be careful and
never run a command you are not sure if it is safe.