SEA-PHAGES | Missing gene in PhagesDB draft genome

Link to this post \| posted 26 Jan, 2024 19:38
hnance@ccga.edu	Hi, It looks like Poultress is missing Gene 33 in the PhagesDB database. The draft genome in PhagesDB counts Gene 32 and the next is 34. Gene 34 in PhagesDB corresponds to the coordinates I have for Gene 33 (start 22659, stop 22994) in my autoannotation file. Is there a reason the database would skip a gene number? This skipped gene number (Gene 33) is missing in Phamerator, too. Thoughts? Thanks!!

Link to this post | posted 26 Jan, 2024 19:38

Hi, It looks like Poultress is missing Gene 33 in the PhagesDB database. The draft genome in PhagesDB counts Gene 32 and the next is 34. Gene 34 in PhagesDB corresponds to the coordinates I have for Gene 33 (start 22659, stop 22994) in my autoannotation file. Is there a reason the database would skip a gene number? This skipped gene number (Gene 33) is missing in Phamerator, too. Thoughts? Thanks!!

Link to this post \| posted 26 Jan, 2024 20:17
debbie	Hi Holly, I don't believe it skipped a number, but rather called something that could not be demonstrated in phamerator. But i don't know what that is. It is not uncommon that numbers of genes don't match between your annotation and what is posted on phamerator. what is posted on phamerator is also what 'feeds' what is posted on phagesDB, so they will indeed match. Hence, I request that one never uses gene numbers (but rather use stops) to identify what gene you are working on. i hope that helps, debbie

Link to this post | posted 26 Jan, 2024 20:17

debbie

Hi Holly,
I don't believe it skipped a number, but rather called something that could not be demonstrated in phamerator. But i don't know what that is. It is not uncommon that numbers of genes don't match between your annotation and what is posted on phamerator. what is posted on phamerator is also what 'feeds' what is posted on phagesDB, so they will indeed match.
Hence, I request that one never uses gene numbers (but rather use stops) to identify what gene you are working on.
i hope that helps,
debbie

Link to this post \| posted 26 Jan, 2024 20:41
hnance@ccga.edu	Hi Debbie, Thanks for the prompt reply. I understand that numbers won't match, and the stop is how they ought to be identified. But I'd never seen a gene number skipped in Phamerator. However, it sounds like it's not a big deal, so I will move ahead! Thanks again for your help!! Holly

Link to this post \| posted 28 Jan, 2024 00:08
cdshaffer	Looking at the database I can see that Gene 33 in Poultris is a tRNA gene, so it does not show up on the list of protein coding genes (i.e. the list on phagesdb). The prediction has the tRNA gene from 21834 to 21936 which is completely within the protein coding gene 32. The database does not give the provenance of the prediction so no way to tell if it was called by tRNA-scan or Aragorn, nor which version of those programs were used. But given the 100% overlap with gene 32 it is probably a false positive result, so I am going to guess tRNA-Scan (no shade on tRNA-scan). tRNA-Scan gives a score with its calls, so its whole design philosophy is to call everything no matter how unlikely and just give the really unlikely ones a very bad score. Just another example of why human manual annotation is still a "Good thing" ™

Link to this post | posted 28 Jan, 2024 00:08

cdshaffer

Looking at the database I can see that Gene 33 in Poultris is a tRNA gene, so it does not show up on the list of protein coding genes (i.e. the list on phagesdb). The prediction has the tRNA gene from 21834 to 21936 which is completely within the protein coding gene 32. The database does not give the provenance of the prediction so no way to tell if it was called by tRNA-scan or Aragorn, nor which version of those programs were used. But given the 100% overlap with gene 32 it is probably a false positive result, so I am going to guess tRNA-Scan (no shade on tRNA-scan). tRNA-Scan gives a score with its calls, so its whole design philosophy is to call everything no matter how unlikely and just give the really unlikely ones a very bad score. Just another example of why human manual annotation is still a "Good thing" ™

Link to this post \| posted 29 Jan, 2024 03:57
debbie	Hi Chris, I went looking for the tRNA using Aragorn. It did not call it. I should have done my due diligence! Holly - check out this paper for consideration: Bacteriophage tRNA-dependent lysogeny: requirement of phage-encoded tRNA genes for establishment of lysogeny https://pubmed.ncbi.nlm.nih.gov/38236026/ I am not suggesting that your genome has a legit tRNA, but this paper describes the first case that we have published where a tRNA is found in the reverse direction while a protein coding gene is in the forward direction. Great classroom conversation! debbie

Link to this post | posted 29 Jan, 2024 03:57

debbie

Hi Chris,
I went looking for the tRNA using Aragorn. It did not call it. I should have done my due diligence!
Holly - check out this paper for consideration: Bacteriophage tRNA-dependent lysogeny: requirement of phage-encoded tRNA genes for establishment of lysogeny
https://pubmed.ncbi.nlm.nih.gov/38236026/
I am not suggesting that your genome has a legit tRNA, but this paper describes the first case that we have published where a tRNA is found in the reverse direction while a protein coding gene is in the forward direction. Great classroom conversation!
debbie

Link to this post \| posted 29 Jan, 2024 10:42
hnance@ccga.edu	Thanks for looking into this! I will share the attached paper with my students as a great reminder for why we annotate. Thanks again! Holly

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Missing gene in PhagesDB draft genome