Ref seq/Gene bank accession to Entrez id for cluster profiler

I have a list id of GenBank accession (protein) for different bacterial species (these are non model bacterial species). The next step is to do GSEA for these proteins. I tried to convert GenBank accession to entrez id, But unfortunalt, I couldnt find the respective id in the NCBI website. Some of the ids are:

> QQR17398.1 QQR17399.1 QQR19149.1 QQR17404.1 QQR17411.1 QQR17417.1
> QQR17418.1 QQR17421.1 QQR17422.1 QQR17448.1 QQR17450.1 QQR17452.1
> QQR17453.1 QQR17457.1 QQR17460.1

How do i convert these ids suitable for ClusterProfiler.

Any help would be really helpful.

idconversion ncbi clusterprofiler genebank

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updated 2.7 years ago by GenoMax

• written 2.7 years ago by mail2steff

1 answer

Using EntrezDirect:

$ esearch -db protein -query QQR17398 | esummary | xtract -pattern DocumentSummary -element Id
1957959289

For more than one ID use epost. Put id's in a file one per line and then do:

$ epost -db protein -format acc -input id_file | esummary | xtract -pattern DocumentSummary -element Id,Caption
1957961040      QQR19149
1957959308      QQR17417
1957959302      QQR17411
1957959295      QQR17404
1957959290      QQR17399
1957959289      QQR17398

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written 2.7 years ago by GenoMax