SEA-PHAGES | Tomas tRNA error

Link to this post \| posted 19 Nov, 2021 14:52
lhughes	I'm getting the following error back from the Phamerator import process for SEA_TOMAS_193 (Tomas_TRNA_40): "ERROR: Evaluation ID: TRNA-EVAL-018. Status: error. Definition: Check if the tRNA coordinates appear to match the Aragorn or tRNAscan-SE prediction(s) for SEA_TOMAS_193 (Tomas_TRNA_40). The tRNA feature is expected to have coordinates that match Aragorn or tRNAscan-SE. Result: The tRNA coordinates (99205, 99279) appear to be incorrect. Left coordinate looks correct. Right coordinate should be moved left by 3 base(s). Status was changed from 'warning' to 'error' automatically due to no interactivity." This tRNA does not show in the web-based Aragorn output. It has an infernal score of 38 in tRNA-Scan. When I check the DNA Master file, the coordinates are different (99206-99279) so am confused by the message saying the left coordinate is correct (the message has a different number than my file) and that makes me question exactly what coordinate is meant by the suggestion to move the right coordinate to the left by 3. (In looking at this, I note that moving the coordinate left by one would leave a "CC" as the last two bases of the tRNA, which would seem to be in keeping with what would likely be expected based on the diagrams in the guide.) I'm attaching a screenshot of the current call in the context of the genome sequence. Suggestions on getting this right so it will import into Phamerator? Lee 263Kb

Link to this post | posted 19 Nov, 2021 14:52

I'm getting the following error back from the Phamerator import process for SEA_TOMAS_193 (Tomas_TRNA_40):

"ERROR: Evaluation ID: TRNA-EVAL-018. Status: error. Definition: Check if the tRNA coordinates appear to match the Aragorn or tRNAscan-SE prediction(s) for SEA_TOMAS_193 (Tomas_TRNA_40). The tRNA feature is expected to have coordinates that match Aragorn or tRNAscan-SE. Result: The tRNA coordinates (99205, 99279) appear to be incorrect. Left coordinate looks correct. Right coordinate should be moved left by 3 base(s). Status was changed from 'warning' to 'error' automatically due to no interactivity."

This tRNA does not show in the web-based Aragorn output. It has an infernal score of 38 in tRNA-Scan.

When I check the DNA Master file, the coordinates are different (99206-99279) so am confused by the message saying the left coordinate is correct (the message has a different number than my file) and that makes me question exactly what coordinate is meant by the suggestion to move the right coordinate to the left by 3. (In looking at this, I note that moving the coordinate left by one would leave a "CC" as the last two bases of the tRNA, which would seem to be in keeping with what would likely be expected based on the diagrams in the guide.)

I'm attaching a screenshot of the current call in the context of the genome sequence.

Suggestions on getting this right so it will import into Phamerator?

Lee

Link to this post \| posted 19 Nov, 2021 16:11
debbie	Lee, Great forum post. Thanks for having a complete set of data. You are correct that the checker message is confusing. Thanks for reviewing. I think that this tRNA is legit and the coordinates are 99206-99276, tRNA-Gln(gat). There is no way around this in the checker and I am will contact Christian to push this one through. Sometimes, you may receive additional error message, but just ignore. it is ready to go in. Best, debbie

Link to this post | posted 19 Nov, 2021 16:11

debbie

Lee,
Great forum post.
Thanks for having a complete set of data.
You are correct that the checker message is confusing. Thanks for reviewing. I think that this tRNA is legit and the coordinates are 99206-99276, tRNA-Gln(gat). There is no way around this in the checker and I am will contact Christian to push this one through. Sometimes, you may receive additional error message, but just ignore. it is ready to go in.
Best,
debbie

Link to this post \| posted 19 Nov, 2021 16:19
lhughes	Awesome! Thanks, Debbie. Lee

Link to this post \| posted 19 Nov, 2021 16:52
cdshaffer	pdm_utils uses Biopython numbering system which is based on python. This system uses zero based counting (the first position is 0) with an "open right end" (the right coordinate is the 1st position after the region). So base numbers for gene positions will not be the same numbers in PDM_utils and DNA Master even though they mark the same region. As a biologist you can think of this as DNA Master is numbering the bases and PDM_utils is numbering the phosphate backbone and always assuming there is a 5' phosphate. So the "base" numbers (99206-99279) are actually marking out exactly the same region as the "phosphate" numbers (99205, 99279). Here is a link to a BioStars page with pictures and more details which show how these two numbering systems relate to each other: https://www.biostars.org/p/84686/ However, while the above explains the difference in the coordinates it does not explain the "move the end 3 bases". Here I believe PDM_utils is just going on the literal tRNA Scan results and has not done any programing to correct the end as should be done manually for all tRNA Scan results (For those unaware see this article in the Bioinformatics guide.) So, if you did do the manual trimming as described your result is better than PDM_utils and I would just ignore its warning and submit. I would also send an email to Deb, Christian and Lawrence that the manually trimmed tRNA at 99206-99279 is indeed correct even though it is failing PDM-utils.

Link to this post | posted 19 Nov, 2021 16:52

cdshaffer

pdm_utils uses Biopython numbering system which is based on python. This system uses zero based counting (the first position is 0) with an "open right end" (the right coordinate is the 1st position after the region). So base numbers for gene positions will not be the same numbers in PDM_utils and DNA Master even though they mark the same region. As a biologist you can think of this as DNA Master is numbering the bases and PDM_utils is numbering the phosphate backbone and always assuming there is a 5' phosphate.

So the "base" numbers (99206-99279) are actually marking out exactly the same region as the "phosphate" numbers (99205, 99279). Here is a link to a BioStars page with pictures and more details which show how these two numbering systems relate to each other: https://www.biostars.org/p/84686/

However, while the above explains the difference in the coordinates it does not explain the "move the end 3 bases". Here I believe PDM_utils is just going on the literal tRNA Scan results and has not done any programing to correct the end as should be done manually for all tRNA Scan results (For those unaware see this article in the Bioinformatics guide.) So, if you did do the manual trimming as described your result is better than PDM_utils and I would just ignore its warning and submit. I would also send an email to Deb, Christian and Lawrence that the manually trimmed tRNA at 99206-99279 is indeed correct even though it is failing PDM-utils.

Link to this post \| posted 19 Nov, 2021 17:22
debbie	Thanks Chris!

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Tomas tRNA error