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Met vs Ile2

| posted 03 Jun, 2022 13:53
I am attempting to submit C1 phage Jedediah, but when it goes through the file checker, I get the following error:

ERROR: Evaluation ID: TRNA-EVAL-011. Status: error. Definition: Check that the annotated amino acid is consistent with the prediction(s) made by Aragorn and/or tRNAscan-SE for SEA_JEDEDIAH_180 (Jedediah_TRNA_24). The tRNA feature is expected to have a correct isotype (amino acid) prediction. Result: The annotated isotype (Ile) is inconsistent with Aragorn (Met) and tRNAscan-SE (Ile2). Status was changed from 'warning' to 'error' automatically due to no interactivity.

The problem is, it IS annotated as Ile2, not Ile. I even re-typed it to be sure. The Bioinformatics Guide says to annotate this as Ile2 (tRNAScan's call, not Aragorn's call of Met), but I also see that other C1s, such as Khaleesi, TinyTim, and McWolfish all call this Met. I re-ran Khaleesi through tRNAScan-SE, and it also calls this Ile2, even though the final GenBank version calls it Met.

What am I missing? Should I call this Met?
| posted 03 Jun, 2022 20:28
If tRNAscan-SE predicts it as an Ile2, that is what should be annotated. The flat file that was uploaded to PhagesDB has the following for the gene in question:

gene 97158..97230
tRNA 97158..97230

The inconsistency between the product/note fields is what causes the error during flat file QC. If you adjust the annotation such that these fields are in agreement, the error should go away.


| posted 03 Jun, 2022 21:08
Thank-you, Christian! I see that now in my flat file. It's weird though, because the DNA Master file has "tRNA-Ile2(cat)" in the product field (and properly in the Documentation), so I don't know why it's getting changed in the flat file. Maybe I can just edit the flat file directly and resubmit; the sub file appears accurate.

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