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

Link to this post | posted 09 Feb, 2024 21:52

debbie

Hi Emily, Both are good questions. For the first gene, the coding potential on the GeneMark output is rather robust upstream of 37. How would you evaluate the ability of that gene to start if you are evaluating a start at base 1. What do you want to see upstream of a start to evaluate the start? How would you do that in this case? Why do you say that RBS only favors the second start? For the second gene, how is that gene going to be made? What favors the best production of that gene? Keep thinking! What did you professor have to say? best, debbie Edited 09 Feb, 2024 21:54

Link to this post | posted 09 Feb, 2024 03:37
debbie	Hi Brandon, More information is needed. What gene (please include coordinates) and genome are your inquiring about? thanks, debbie

Link to this post | posted 09 Feb, 2024 03:33
debbie	Hi ACMPhageHunters, More information is needed to help. What gene (please provide coordinates) and genome are you inquiring about? Thanks, debbie

Link to this post | posted 08 Feb, 2024 21:00
debbie	Hi Nancy, I used the posted file and was able to auto-annotate. Were other students able to annotate. sounds like something is up with the student's installation of DNA Master, or their Windows is interpreting the file as something it is not. debbie

Link to this post | posted 08 Feb, 2024 18:12
debbie	Hi Nancy, Let's see if I can help. But I need more information. Are you in DNA Master, file -> open -> FastA multiple sequence file? Is the file the .fasta file for your phagesDB phage page. Is it a text file? Can you open a different dna master file and navigate around it. Have you tried more than 1 different fasta file? debbie

Link to this post | posted 07 Feb, 2024 23:42
debbie	Adam, What do you want to call here? What is your evidence? debbie

Link to this post | posted 07 Feb, 2024 12:44
debbie	Adam, In the paper referred to the Bioinformatics Guide, the TAC 'template' is X_XX.Y_YY.Z. You have not provided enough information for me to look quickly, but check the guide to interpret the '_ 'and '.'s If your CCCTTTT lines up correctly for a -1 Frameshift, you have a canonical programmed ribosomal slippage. You also used an abbreviation 'PF' that i don't recognize. debbie