SEA-PHAGES | PECAAN and tRNA notes problem?

Link to this post \| posted 22 Jun, 2018 03:57
lhughes	I am working on 4 Cluster BK1 genomes which all have lots of tRNAs. When I reached my final review of the genomes and comparisons of their labeled functions, including tRNA, I was surprised to find that the tRNA notes were not matching the tRNA output from Aragorn/tRNAScan. Basically, what I think is happening is that the exported notes are showing the Codon sequence, not the Anticodon sequence. For example, in Annadreamy, the first tRNA (4218-4145 Reverse) shows the anticodon as GGT when you look at the Aragorn/tRNA scan information, but the output from PECAAN gives it as ACC. The reason I noticed it originally was because I had downloaded another BK1, Blueeyedbeauty, sometime last year and it had GGT in the output (but if I re-download now it gives me ACC). Please help me figure this out. These genomes each have over 35 tRNAs in them so I need to make sure I'm getting them in the correct format (and hopefully this is not an issue for others who've done tRNA's recently). Thanks, Lee

Link to this post | posted 22 Jun, 2018 03:57

I am working on 4 Cluster BK1 genomes which all have lots of tRNAs. When I reached my final review of the genomes and comparisons of their labeled functions, including tRNA, I was surprised to find that the tRNA notes were not matching the tRNA output from Aragorn/tRNAScan. Basically, what I think is happening is that the exported notes are showing the Codon sequence, not the Anticodon sequence.

For example, in Annadreamy, the first tRNA (4218-4145 Reverse) shows the anticodon as GGT when you look at the Aragorn/tRNA scan information, but the output from PECAAN gives it as ACC.

The reason I noticed it originally was because I had downloaded another BK1, Blueeyedbeauty, sometime last year and it had GGT in the output (but if I re-download now it gives me ACC).

Please help me figure this out. These genomes each have over 35 tRNAs in them so I need to make sure I'm getting them in the correct format (and hopefully this is not an issue for others who've done tRNA's recently).

Thanks,
Lee

Link to this post \| posted 22 Jun, 2018 16:45
cdshaffer	Yes, you are correct, in every case I have worked with lately Pecaan is giving the codon in the downloaded notes (i.e the reverse complement of the anti-codon reported by tRNA-scan). I always change the final notes back to the anti-codon before creating the genbank submission file. Since Pecaan reports the codons in uppercase, I make the anti-codons lower case which helps me keep track if that step has been completed and matches the examples from the online documentation. In genbank the "tRNA-Thr(ggt)" info ends up in the "Notes" field. There is no official standard for that field in the official documentation here. So I think the important thing is to have everything from the SEA-Phages use the policy as stated in the online docs linked above.

Link to this post | posted 22 Jun, 2018 16:45

cdshaffer

Yes, you are correct, in every case I have worked with lately Pecaan is giving the codon in the downloaded notes (i.e the reverse complement of the anti-codon reported by tRNA-scan). I always change the final notes back to the anti-codon before creating the genbank submission file. Since Pecaan reports the codons in uppercase, I make the anti-codons lower case which helps me keep track if that step has been completed and matches the examples from the online documentation.

In genbank the "tRNA-Thr(ggt)" info ends up in the "Notes" field. There is no official standard for that field in the official documentation here. So I think the important thing is to have everything from the SEA-Phages use the policy as stated in the online docs linked above.

Link to this post \| posted 22 Jun, 2018 17:17
debbie	Hi. I sent an email to Dex and Claire about this. Technically, we are not reporting codon or anti-codon but rather the DNA sequence that makes the anti-codon. So I can see why this gets confusing. Edited 22 Jun, 2018 19:42

Link to this post \| posted 22 Jun, 2018 18:04
lhughes	Ok - thanks. I'm glad it wasn't just me. I'll make the updates manually in the files that I am submitting. Lee

Link to this post \| posted 02 Jul, 2021 16:52
ClaireRinehart	PECAAN has been modified to output the tRNA report so that it now passes the QC workflow.

Link to this post \| posted 07 Jul, 2021 18:18
cdshaffer	Claire and (presumably) Dex and any other coders, thanks for fixing this bug and all the work you do to keep updating and improving PECAAN.

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PECAAN and tRNA notes problem?