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Where to find full operon annotations of E coli

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!

gtf annotation gff bed
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updated by massa.kassa.sc3na massa.kassa.sc3na • written by noodle noodle

1 answer

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 :)

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written by massa.kassa.sc3na 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.

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written by massa.kassa.sc3na massa.kassa.sc3na

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