SEA-PHAGES | Met vs Ile2

Link to this post \| posted 03 Jun, 2022 13:53
c.sunnen	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?

Link to this post | 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?

Link to this post \| posted 03 Jun, 2022 20:28
chg60	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 /gene="180" /locus_tag="SEA_JEDEDIAH_180" tRNA 97158..97230 /gene="180" /locus_tag="SEA_JEDEDIAH_180" /product="tRNA-Ile" /note="tRNA-Ile2(cat)" 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. Best, Christian

Link to this post | posted 03 Jun, 2022 20:28

chg60

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
/gene="180"
/locus_tag="SEA_JEDEDIAH_180"
tRNA 97158..97230
/gene="180"
/locus_tag="SEA_JEDEDIAH_180"
/product="tRNA-Ile"
/note="tRNA-Ile2(cat)"

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.

Best,

Christian

Link to this post \| posted 03 Jun, 2022 21:08
c.sunnen	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. Thank-you! Nikki

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Met vs Ile2