smallRNA prediction and InterGenic Regions(IGRs) finding

Question

[venkatdadi9]

Hi All,

I have two questions.

1. 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.
2. Is there any tool to find intergenic regions (IGRs) in a given bacterial genome.

Your answers would very helpful to my work.

Regards,
Venkat

Answer 1

[bioslayer]

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?