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tRNA in EA2 and EA5 phages called by tRNAscan SE but not aragorn

| posted 18 Jul, 2018 19:08
Thus far it appears that none of the EA phages are reported to contain tRNAs. We recently finished annotating an EA2 bacteriophage Andromedas, that had a potential tRNA that was not called by Aragorn, but was called by tRNA scanSE but bc it had an infernal score of 38 and we decided to not include it in our annotation after looking at the structure of the anticodon loop.

I am currently checking an EA5 phage, Neferthena, and again we found a potential tRNA that was not called by Aragorn, but was called by tRNAscanSE, this time the infernal score is 52.

I have attached screen shots of the two tRNAs from PECAAN, and would like a second opinion on whether or not to keep the tRNA from Neferthena, the anti-codon loop does not look canonical to me, but I don't have much experience looking at these structures.

Any advice is appreciated.
Thank you,
| posted 22 Jul, 2018 02:35
I would call both of these. They meet the cut-off criteria that we have set forth.
for Neferthena, it looks like the end are called correctly.
For Andromedas, you will need to trim the last 2 bases (GA).
Edited 22 Jul, 2018 10:54
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