Operon Prediction for prokaryotes

Question

[ARich]

Dear Biostarizens,

I am currently working on operon prediction project. In this work i would like to find of similar cooperonic organization in prokaryotic genomes. Can someone suggest me a workflow paper or tools which i can use to perform my analysis.

Thank you in advance

[Kevin Blighe]

Good morning / afternoon,

You have not stated the type of data that you currently have; however, you can try Rockhopper for RNA-seq data, and here is the related publication: A computational system for identifying operons based on RNA-seq data.

[ARich]

Dear Kevin,

Thank you for your reply, its actually a genomic data.

[Fatima]

You might be able to make use of regulondb in your pipeline:

http://regulondb.ccg.unam.mx/index.jsp

[ARich]

Thank you but i didnt quite get how can i intergrate regulondb? I am new to this topic, can you expand you answer as to how to intergrate, since i have to pipeline yet. I am still looking for papers and tools to understand this concept.

[Fatima]

I think their website only contains operons in E-coli, but I thought it might be useful for training or test purposes in your project:

Computational predictions:

http://regulondb.ccg.unam.mx/menu/download/computational_predictions/index.jsp

Supported by literature with experimental evidence:

http://regulondb.ccg.unam.mx/menu/download/datasets/index.jsp

Answer 1

[Joe]

If you're just looking for co-occurences of similar operons and clusters, I'd suggest looking at:

• Sibelia and SibeliaZ

• MultiGeneBlast

[ARich]

Thank you for sharing tools name. SibeliaZ is closer to what i was looking for but it works only with closely related species which means it will not be ideal to use where recent common ancestor not exceeding 0.085 substitutions per site.