Where to find full operon annotations of E coli

Question

[noodle]

Hi biostars,

Someone knows where to find a 'full' annotation of operons in E coli in gff/gtf/bed format? By 'full' I mean that, for example, the rRNA loci would be from the pre-rRNA transcript including ETS/ITS. Bonus points if promoters/terminators are also annotated. Thanks!

Answer 1

[massa.kassa.sc3na]

Hi, I think that great place to start would be recent paper titled Escherichia coli transcriptome assembly from a compendium of RNA-seq data sets.

The section (and data) about "Transcription units" might be of special interest (links supplement 5; supplement 6)

Disclaimer: I'm not affiliated with the institution / author. I've just noticed the paper recently and spotted this question today :)

[noodle]

Thanks for pointing this one out, unfortunately it seems the tables are largely incomplete. What I had in mind was more like an heirarchical annotation file of this; https://www.ecocyc.org/genbro/genbro.shtml?orgid=ECOLI&replicon=COLI-K12

[massa.kassa.sc3na]

You mean incomplete in a sense that not all annotated genes are there, or it's more messy than you've expected?

Btw.: AFAIK for ecocyc, you should be able to access the underlying data (https://biocyc.org/download.shtml); but I have not experience beyond this, as our institute does not have a subscription.