5 UTR for bacteria

Question

[kodo64]

I was wondering if there is a way to obtain/predict 5′-UTRs for bacteria given i have RNA seq data, a complete genome sequence of the bacteria as well. There seems to be no databases dedicated to this for prokaryotes. Any tools if available would also be welcome

thanks

Answer 1

[jv]

See https://www.biostars.org/p/209912/#209912 for a previous discussion regarding this question.

tl;dr while you can't as precisely identify transcription start sites with traditional RNA-seq as compared to say TSS-seq or dRNA-seq there are tools that will predict TSS from RNA-seq. Keep in mind you will be largely limited to the distal most TSS for a transcript when predicting TSS from RNA-seq data.

For bacterial data specifically I recommend first reviewing https://pubmed.ncbi.nlm.nih.gov/25947005/

[kodo64]

thanks will check them out