Operon Prediction for prokaryotes
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
2 answers
If you're just looking for co-occurences of similar operons and clusters, I'd suggest looking at:
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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.
Dear Kevin,
Thank you for your reply, its actually a genomic data.
Dear Kevin,
Thank you for the reply its a genomic data.
Please use
ADD COMMENT/ADD REPLYwhen responding to existing posts to keep threads logically organized.SUBMIT ANSWERis for new answers to original question.sorry for the mistake
You might be able to make use of regulondb in your pipeline:
http://regulondb.ccg.unam.mx/index.jsp
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.
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