smallRNA prediction and InterGenic Regions(IGRs) finding
Hi All,
I have two questions.
- I'm going to work on smallRNA prediction in XYZ bactrium. There are number of tools available, using different methods. Can somebody suggest the best tool(s) for smallRNA prediction.
- Is there any tool to find intergenic regions (IGRs) in a given bacterial genome.
Your answers would very helpful to my work.
Regards,
Venkat
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1 answer
I am aware of FeatureExtract and RSAT.
These two frameworks parse an annotated genome file and allow you to select/filter unannotated regions. Therefore they rely on proper annotation as a prerequisite. If your bacterium is E.coli then RegulonDB is a database of experimentally predicted UTR regions for which TSS and other features have been determined in a lab.
What other tools have you tried or experimented with?
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