1) I have tried using Barrnap and Prokka for prokaryote genome annotation. In both cases, I was unable to discover/annotate the 5SrRNA in an unknown/new bacteria assembly. I tried both these methods as well with a known bacteria (that was expected to have two 5SrRNA) and did not come to such results (i.e. could not find any 5SrRNA annotation in the downloaded reference genome). Are there other simple programs/methods to discover 5SrRNA in bacterial genomes? Moreover, is it even possible for a bacteria to not have 5SrRNA?
2) I ran Prokka on a known bacteria genome that supposedly has two copies of 23SrRNA and two copies of 16SrRNA. I found the same results (2 copies of both). Upon further investigation, I noticed that the copies of 23SrRNA are identical to each other and the copies of 16SrRNA are identical to each other. I wanted to ask if this seems feasible that a bacteria sample should have exactly the same rRNA repeated in such manner?
Do you have the
Infernaloptional dependency installed (https://github.com/tseemann/prokka#optional)? The infernal together with Rfam database should be able to find the RNAs.Thanks @massa.kassa.sc3na. Thanks for this suggestion. This time, I reran Prokka using --rfram (prokka --rfram input.fasta). I had the same number of "rRNA" (and they were still 16S and 23S). However, one difference is that I now had 4 "misc_RNA". These had lengths of 292, 384, 320, and 294. There product titles were "5_ureB_sRNA", "tmRNA", "RNaseP_bact_a", "5_ureB_sRNA". I have read that 5S rRNA have length of about 120 nucleotides, so I am assuming these misc_RNA are not 5SrRNA. Even sorting the output (specifically the .TSV) and looking for features around 120 nucleotides, I only see listing for "hypothetical protein" that all have ftype of "CDS". I hope I ran the program correctly and am reading the output correctly. Is it a surprise that I am still not finding any 5srRNA?