How to convert E. coli gene names from biocyc to Ensembl IDs?
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10 months ago
Macspider ★ 3.4k

Hi everyone,

I'm struggling with something that I couldn't anticipate to be so hard to find. I am very new to the _E. coli_ world, having worked my whole life with plants. Hence, please don't judge if this is common knowledge.

I have a list of genes structured like this:

> head(Ctrl)
Code  Gene     GOTerm
1 A0A385XJ53 insA9 GO:0006313
2     A5A605  ykfM GO:0006974
3     A5A615  yncL GO:0005886
....


I would like to extract the Ensembl ID for each gene. I have the following libraries at hand:

library(biomaRt)
library(org.Hs.eg.db)
library(AnnotationHub)
library(ensembldb)


Any quick workaround? Everything I found goes in the other direction (Ensembl to gene name) or is for Human / Mice only.

ENSEMBL biocyc Escherichia coli conversion R • 375 views
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Unfortunately "access programmatically" link on Ensembl bacteria page is generating an error at the moment. There are way too many E. coli genomes around so you will need to pick one when the page works.

You could find a genome you like (from link above). Get the annotation file for it and do the conversions that way.

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Oh, so it's not me, it's the Ensembl bacteria page that is down. For a second I thought I was crazy.

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@Emily_Ensembl says that it takes 1000 queries at a time so 5-6 lookups can do it.