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I'm annotating tRNAs & rRNA genes in a flatworm species using the tools Infernal, RNAmmer & tRNAscan-SE. My plan was to compare the outputs in the hopes that for future worms I could just run Infernal to get all ncRNA annotations but now that I'm looking at results I realize that I am lacking in my knowledge of basic biology.
For the rRNA genes should I expect the same number of copies of each type of subunit (ie. 5s, 18s & 28s)? Also, RNAmmer is annotating '8s' instead of '5s' for the smallest of the subunit components. Is this a problem with my execution of the software? I'm using RNAmmer v1.2 and told it to search for tsu, ssu & lsu from eukaryotes.
Then for tRNAs, tRNAscan-SE is finding 100s of them. But there are only 61 codons, and I think actually there may not be a unique tRNA for every codon due to the wobble base. So is it ok that I am finding many copies of tRNAs in my genome?
Thanks,
John Martin
For the rRNA genes should I expect the same number of copies of each type of subunit (ie. 5s, 18s & 28s)? Also, RNAmmer is annotating '8s' instead of '5s' for the smallest of the subunit components. Is this a problem with my execution of the software? I'm using RNAmmer v1.2 and told it to search for tsu, ssu & lsu from eukaryotes.
Then for tRNAs, tRNAscan-SE is finding 100s of them. But there are only 61 codons, and I think actually there may not be a unique tRNA for every codon due to the wobble base. So is it ok that I am finding many copies of tRNAs in my genome?
Thanks,
John Martin