I am working on Vibrio parahaemolyticus. I have a gene that it is possible might be regulated by small non-coding RNAs. How can I predict possible sRNAs that target the transcript of this gene. Most software offers the opposite of what I want, i.e., they predict targets for small RNAs!
I'm trying to predict bacterial small non-coding RNA in general (Support Vector Machine) but I got more than 8 thousand sequences within intergenic regions alone. Is there a code for aligning these sequences to my transcript?