Link to this post | posted 03 Jul, 2025 23:31
lhughes	Happy to help. There are a lots of "behind the scenes" steps that aren't in those materials, so feel free to ask for other details whenever you have questions. Lee

Link to this post | posted 03 Jul, 2025 20:25

lhughes

Martin and Steve, I use PECAAN primarily in class and we only use DNA Master for the final genome preparation to submit (so the students do all the annotation in PECAAN and then just check the final output in DNA Master). They do use DNA Master for "special projects" after the basic annotation is done (we have dedicated computers in our lab that have DNA Master on them if the student is not able to use it on their own computer). My videos are getting old (I need to redo them and some things might not match the current programs), but they are on YouTube. Here are links: Genemark overview: https://youtu.be/l74Eg8ldd8g PECAAN overview: https://youtu.be/cZ04rdYYaVQ Starterator: https://youtu.be/KMqrZ0eUXOk Gene Start Decisions: https://youtu.be/6_yAlFYzdL8 Gene Function Decisions: https://youtu.be/5ryYsJG-vok Using DNA Master: https://youtu.be/wqTDiJxhe2Q tRNA analysis: https://youtu.be/u5aIjfbi4oM Finalizing Annotation: https://youtu.be/hGu5rZLI7Ys Programmed Translational Frameshift: https://youtu.be/LrZDUSULs3g I also use videos from Pitt: Using HHPRED: https://vimeo.com/428673929 I use the Gene Prediction resources on Qubeshub that the SEA community developed prior to going into the program and decision making slides. That resources is at: https://qubeshub.org/publications/2029/1 I also organize my students annotations using resources in the "Student and Faculty Tools for Generating High-Quality Phage Annotations" on QubesHub at https://qubeshub.org/publications/2048/1 After I finish the basic overview slides about gene prediction is when I first introduce PECAAN to the class. We then have slides that go over the different programs and how they are used to make decisions.(I've added one - the main other slides are links to some of the videos above). It is usually about 4 weeks of training on tools and some practice annotations as a class before I have students start doing their own gene annotations. I hope this information is helpful, although I recognize that it probably doesn't make perfect sense the way I described it! Let me know any questions that you have. Lee 229Kb

Link to this post | posted 16 Jun, 2025 13:48
lhughes	All BN phages to date contain the following slippery sequence (GGGAAAC)in the tail assembly chaperone that gives a -1 slippage. However, this programmed translational frameshift has not been called previously so may not show when doing comparisons with previously annotated phages. Edited 16 Jun, 2025 13:49

Link to this post | posted 16 Jun, 2025 13:46
lhughes	The Cluster BJ phages identified to date have a -1 slippage at the following sequence (GGGAAAC)in the tail assembly chaperone. Edited 16 Jun, 2025 13:50

Link to this post | posted 16 Jun, 2025 13:40
lhughes	debbie Lee, It sounds correct to me! XXXYYYZ is always a winner! debbie Thanks, Debbie!

Link to this post | posted 12 Jun, 2025 19:43

lhughes

The following sequence is called as the slippery sequence in the cluster BJ phage Dubu (GGGAAAC, in Dubu_13), which matches the XXXYYYZ pattern that has been called elsewhere (example is the BK1 phage as discussed here: https://seaphages.org/forums/topic/5168/?page=1). BN phages have a TAC in the same pham as the TAC of Dubu (CF phage also have this pham, but only one has the frameshift called, Jflix2_18 which has GGGTTTC. None of the other CF phage have the XXXYYYZ at that location). The frameshift has not been previously called in this cluster, but all 10 members of the cluster contain this pham (two genes upstream of the tapemeasure) and the GGGAAAC is conserved in all of them. I am QCing Greenbelt, which my students just annotated, and they chose to call this frameshift. I believe that they are correct and plan to include this in the final file. Assuming there is nothing I am missing, I also plan to add a note in the cluster-specific forum page for BN (as well as BJ, which doesn't currently have a TAC note) to provide information about looking for this frameshift. How does this sound to everyone? Let me know if you need more information. Lee

Link to this post | posted 21 Jan, 2025 00:14
lhughes	rocky2 I remember seeing someone presenting a PowerPoint or Google Slides template for annotating each gene. It's a datacard template that includes the gene documentation. Can someone post it here? -Rocky There are templates in QUBESHUB in the "Student and Faculty Tools for Generating High-Quality Phage Annotations" resource. http://dx.doi.org/10.25334/WDMM-SV47

Link to this post | posted 03 Apr, 2024 13:47
lhughes	It opened fine for me just now. Lee

Link to this post | posted 06 Feb, 2024 16:44

lhughes

Hi Adam and Debbie, I did a very quick look at this yesterday. There are 32 phages in BD2, but only 13 had this particular gene call based on Phamerator data (and 3 of those, including Superstar are draft annotations). I only did a quick glance through them and didn't see a clear pattern on the overlap sizes that have been called, but I didn't really have a chance to look into them in detail. Please continue to share your progress here. We are annotating the two other draft genomes at UNT right now. Thanks, Lee

Link to this post | posted 26 Jan, 2024 14:51
lhughes	Fred - my understanding is that each program determines how to label the different frames independently, so there is no "standard" for which is going to be -1, etc. You need to determine which aligns with which each time you compare the data from two different programs to make sure you are comparing apples to apples. Lee