I'm searching for these genes in bacterial genomes. So far I have been using Modomics and Ecocyc. However Modomics contains proteins involved in RNA modification only and Ecocyc is incomplete. I'd like to search also for other genes involved in ncRNA metabolism (e.g.: RNases, cca, aminoacyl tRNA synthetases...) Moreover I can use only genes of E. coli from these databases. It would be useful to have reference sequences of more species.
Thank you for any suggestions
you can use Bacterial Small Regulatory RNA Database.
http://www.bac-srna.org/BSRD/index.jsp
Dear Kamila
Apart from the aformentioned suggestions, the NCBI GenBank lists the ncRNA records when you search through batch entrez. That will also allow you toidentify ncRNAs linking them with references in a slidable window.
Best
Prash
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