SEA-PHAGES | Cluster FC in Phamerator

Link to this post \| posted 12 Feb, 2024 16:28
eagodin	Good morning, We are annotating an FC cluster phage this semester, and all phages in the FC cluster are in draft mode in Phamerator, however, most of these phages have been QCed already. Is this a Phamerator update issue that will hopefully be fixed moving forward? Thank you! Edited 12 Feb, 2024 16:28

Link to this post \| posted 12 Feb, 2024 19:29
debbie	Hi Elizabeth, The issue is that Cluster FC phages have just recently been found to have direct terminal repeats. Originally they were thought to be circularly permuted, which created a different sequence and end determination. What that means is that all genomes with old (incorrect) sequences at the ends) had to be reposted. That means that all phages look like draft in phamerator. It also means that the 3 that were final (Atuin, Racecar and Mimi) have to be converted to their new sequence. and revisions sent to GenBank and phamerator. That work is not quite done. But my challenge to you and your students is that, when the first 3 were done, the comparative data was sparse or non-existent. You have the opportunity to make calls with significant amounts of data and no distractions of what others have interpreted. Currently, with the data for 8 Cluster FC genomes, better information can be gathered from the comparisons - like starterator - to make really good choice about is it a gene, what is its start, and what is its function, without contradicting what others said with less than optimal (or no) comparative data available. Consider embracing this challenge because it is all good! debbie

Link to this post | posted 12 Feb, 2024 19:29

debbie

Hi Elizabeth,
The issue is that Cluster FC phages have just recently been found to have direct terminal repeats. Originally they were thought to be circularly permuted, which created a different sequence and end determination. What that means is that all genomes with old (incorrect) sequences at the ends) had to be reposted. That means that all phages look like draft in phamerator.
It also means that the 3 that were final (Atuin, Racecar and Mimi) have to be converted to their new sequence. and revisions sent to GenBank and phamerator. That work is not quite done.

But my challenge to you and your students is that, when the first 3 were done, the comparative data was sparse or non-existent. You have the opportunity to make calls with significant amounts of data and no distractions of what others have interpreted. Currently, with the data for 8 Cluster FC genomes, better information can be gathered from the comparisons - like starterator - to make really good choice about is it a gene, what is its start, and what is its function, without contradicting what others said with less than optimal (or no) comparative data available. Consider embracing this challenge because it is all good!

debbie

Link to this post \| posted 13 Feb, 2024 03:29
eagodin	Thanks for the update, Debbie! Does this mean that we shouldn't use Atuin, Mimi, or Racecar as comparators at all, since the sequences were incorrect? I think my students are up for a good challenge, but will certainly reach out with any questions that come up. Liz

Link to this post \| posted 13 Feb, 2024 14:57
DanRussell	eagodin Thanks for the update, Debbie! Does this mean that we shouldn't use Atuin, Mimi, or Racecar as comparators at all, since the sequences were incorrect? I think my students are up for a good challenge, but will certainly reach out with any questions that come up. Liz Hi Liz, Just to be clear, the sequences were correct in the sense that all the bases were right. The change was just where Base 1 was, and duplicating a portion of the genome. (Not changing any individual bases or anything.) So everything should be fine/comparable, including the original annotations of those complete ones, but numbers will have changed. –Dan

Link to this post | posted 13 Feb, 2024 14:57

DanRussell

eagodin
Thanks for the update, Debbie! Does this mean that we shouldn't use Atuin, Mimi, or Racecar as comparators at all, since the sequences were incorrect? I think my students are up for a good challenge, but will certainly reach out with any questions that come up.
Liz

Hi Liz,

Just to be clear, the sequences were correct in the sense that all the bases were right. The change was just where Base 1 was, and duplicating a portion of the genome. (Not changing any individual bases or anything.) So everything should be fine/comparable, including the original annotations of those complete ones, but numbers will have changed.

–Dan

Link to this post \| posted 14 Feb, 2024 01:40
eagodin	Thanks for the clarification, Dan! -Liz Edited 14 Feb, 2024 01:41

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Cluster FC in Phamerator