I am using RNAmmer version 1.2, available after sign-up at http://www.cbs.dtu.dk/services/RNAmmer/, for download from an e-mailed link. I've followed updated instructions at https://blog.karinlag.no/category/rnammer/ and www.cbs.dtu.dk/services/RNAmmer/instructions.php As such I do not observe any run errors.
In the RNAmmer paper at https://www.ncbi.nlm.nih.gov/pubmed/17452365, it says that for eukaryotes (which fungi are), 5.8S is not yet predictable, but the remaining LSU components - 5S, and 28S can be predicted, and so can the 18S SSU.
What I am confused about is that RNAmmer ver1.2 returns predictions for an "8S_rRNA" subunit. But I cannot find anything about an "8S_rRNA" subunit. Am I mistaken?
I was suspicious this RNAmmer ver1.2 may predict 5.8S_rRNA, not possible with ver1 (?), and this 8S_rRNA is a systematic typo error. So, I searched an example sequence prediction at NCBI BLAST against nr database, but it only yielded a pretty good match to a fungal "5S ribosomal RNA rRNA" - Score = 209 bits (113), Expect = 9e-5, Identities = 115/116 (99%), Gaps = 0/116 (0%).
So back to square one - I've contacted the authors Peter Fischer Hallin and Karin Lagesen about this observation. Since RNAmmer is not really supported formally, I am not hopeful of a prompt reply. Could someone on this forum please throw light on my problem, and help clear my confusion? Thanks!
1 answer
Look at figure 1 from the RNAmmer paper, more precisely, look at panel G title. Also, see this quote from RNAmmer site:
The RNAmmer 1.2 server predicts 5s/8s, 16s/18s, and 23s/28s ribosomal RNA in full genome sequences.
It seems to me at some point they used 8S as synonym to eukariotic 5S, but later dropped it, forgetting some bits here and there.
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