Hello!
Could someone suggest a tool for prediction of circRNA using as input a specific genomic sequence (or the genomic coordinates of a single mammalian gene)?
I want to know if a particular Mus musculus (mouse) gene can transcribe circRNAs.
I don't want to analyze the entire mouse transcriptome, but rather a particular gene.
What would be the tool for that?
Thank you !
Hi Geraldo,
You might want to look at some tools developed by the Salzman lab, at Stanford. She is one of the pioneers in circRNA: http://salzmanlab.stanford.edu/software
Best,
Stephano.
Hi
I am afraid that without transcriptome data, any de novo prediction for circRNA could fail. Back splicing is very dynamic event, and it is conditioned by the cell type, environmental conditions and external stimuli. You can always go to databases of circRNAs like circBase and try to see if your gene of interest has already characterized circRNAs.
Best.