Link to this post | posted 03 Mar, 2024 11:03

debbie

Thank Claire, After reviewing your data, i am beginning to believe that conformity is not all that its cracked up to be! I agree with your assessment of gene 18 in Luxx. the 4-base overlap is much more convincing than the bigger overlap. We used alpha-fold to fold the longer version of 18 and the lysin, and no structures were observed to be helpful. So while the data may not change for a while, I agree that the start choice that Claire points out (the 4 base overlap) is a better choice. For genes 21 and 22, I like the original 'conformity' calls because of coding potential evaluations. So call upon your best gene evaluation skills and make your best call. Please draw attention to these genes in your cover letter, so that the QCer can also evaluate. Anyone want to do some bench work?!! Best, debbie

Link to this post | posted 29 Feb, 2024 02:40
debbie	Check HHPred results. Yes, they are not in the typical synteny. Though it is not common, it is not uncommon. debbie

Link to this post | posted 22 Feb, 2024 21:48
debbie	I changed the approve function to say: "Typically has HEXXH motif but other metalloprotease motifs (e.g. "ExnHxHx7Sx2D)" debbie

Link to this post | posted 21 Feb, 2024 18:20
debbie	Hi Beth, What phage are you annotating? Could you provide the phamerator gene number and its stop codon. Thanks, debbie

Link to this post | posted 17 Feb, 2024 13:54
debbie	Fred, I think you have a good choice! Best, debbie

Link to this post | posted 16 Feb, 2024 17:06
debbie	H John, This is on my plate to fix. They will be in phamerator soon debbie

Link to this post | posted 15 Feb, 2024 20:12
debbie	I don't think that it matters if they are ATG, GTG, or TTG. Starts are starts and the amino acids chain start with an fMet. debbie

Link to this post | posted 15 Feb, 2024 15:17

debbie

Hi Fred, The right arm of some of our well studied mycobacteriophages defy common annotation practice. Here is how I look at it. We have published papers where the right arm has no coding regions because there are RNAs expressed. The paper about mycobacteriophage Giles has the best display of bench data that we have. I am always cautious to not overcall the right end of a genome. I think these are some of the stats to consider: This ORF is only found in Cluster A4s. Phamerator has it as 17/134 genes annotated. Are they all drafts? How many of them have the nucleotide sequence? How conserved is it? Could it be something other than a protein coding sequence? You mention no coding potential. Nor, is it easy to see how this gene would get easily made. Check out other cluster A phages like L5 or D29 and note they are not over-calling this region. Also, what is the risk if you delete it? Do you think a researcher who want to investigate lemur_85 isn't going to find this segment of DNA in Alberto7. Most important is that you can support whichever call that you make. Looking at all of the data is and not what others have done will get you to a best answer. Good luck as you make this decision! debbie

Link to this post | posted 14 Feb, 2024 20:19
debbie	Hi Brandon, I think that what you are asking me is to decide if the appropriate functional call is Holliday junction resolvase or RuvC-like resolvase, yes? What do you think it should be? What is your evidence Have you read any papers about them? How are those two functions related? What did your professor think? 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