Operon Prediction With Rna-Seq

Question

[Pasta]

Hi,

More like a brainstorming here than a question. I would like to know about your thoughts.

I'd like to make operon prediction on RNA-seq data but I dont think that any tool exist for that. The operon prediction of I am working on is not yet in public DB.

So I thought about developing my tool. The idea is to first define transcription units (TU) when coverage is above a certain threshold. Then check if my TUs encompass several ORFs and are in the same orientation, if so call it an operon.

What do you think of that idea? Should it be enough ? Any thoughts '

Thanks for your input

Answer 1

[Daniel Standage]

Imagine if you had two operons right next to each other--how close do the operons need to be before you stop calling it two operons and begin calling it one operon?

What if you have several ORFs in an operon, all of which have sufficient coverage (above the threshold), but the ORFs on the 5' end are expressed 10x more than the ORFs on the 3' end. Do you still call it a single operon, or do you split it into two operons based on the expression levels?

Those are just two things that came to mind.