How to track which protein ID is linked to which gene ID with rentrez
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4.2 years ago
s_herrera ▴ 10

I have a bunch of protein IDs and I want to fetch the corresponding coding sequences (CDSs) without loosing the protein ID. I have managed to download the corresponding CDSs, but unfortunately, CDSs IDs are very different from protein IDs in NCBI.

I have the following R code:

library(rentrez)
Prot_ids <- c("XP_012370245.1","XP_004866438.1","XP_013359583.1")
links <- entrez_link(dbfrom="protein", db="nuccore", id=Prot_ids, by_id = TRUE)

And then, I used this command to "match" protein IDs with CDS IDs:

lapply(links2, function(x) x$links$protein_nuccore_mrna)

[[1]]
[1] "820968283"

[[2]]
[1] "861491027"

[[3]]
[1] "918634580"

However, as you can see the argument 'by_id=TRUE' just make a list of three elink objects but now I have lost the protein IDs.

I would want something like:

Protein ID XP_012370245.1 XP_004866438.1 XP_013359583.1
CDS ID XM_004866381.2 XM_012514791.1 XM_013504129.1

Any suggestion is very welcome, thanks!!

R rentrez NCBI • 1.1k views
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