Link to this post | posted 11 Jun, 2023 14:06
scaruso	Hello, I usually use DNAM for teaching and PECAAN for QC, but with the current DNAM connection issue, I may have to use PECAAN for teaching in a week or two in a class of 18. I can come up with something, but if I don't have to reinvent the wheel, I would rather not. So, does anyone have a way of teaching it/with it that they like and want to pass on? Thanks! Steve

Link to this post | posted 12 Jun, 2023 12:21
kbutela	Hi Steve- I have a manual update workaround that is not pretty to set up but seems to be functional. I'll reach out via email to set up a time where we can Zoom to discuss. I don't quite have written instructions ready to distribute, but more people testing the strategy will help. Thanks!

Link to this post | posted 12 Jun, 2023 13:39
lhughes	Hi Steve, If you can't get the DNAM workaround from Kristen to work for your class, I'm happy to share how we use PECAAN in our classes (slides and other resources). We use PECAAN first in our annotation classes. Lee

Link to this post | posted 29 Jun, 2025 14:50

mespariz

lhughes Hi Steve, If you can't get the DNAM workaround from Kristen to work for your class, I'm happy to share how we use PECAAN in our classes (slides and other resources). We use PECAAN first in our annotation classes. Lee Lee, Thank you for sharing these resources. I came across your message from two years ago and found it very relevant to our current situation. If the offer still stands, I would be extremely grateful to receive your PECAAN slides and any additional teaching materials you've used in your classes. We've experienced ongoing challenges with DNAM installations in our cohort, and I'm evaluating whether PECAAN could serve as a comprehensive replacement for our entire workflow. Specifically, I'm wondering if it can handle the complete workflow, including QC submission and "Review to Improve" step. If you've made any updates to your approach since your original post or have insights about potential limitations, I would greatly appreciate your guidance. Thank you for your time and expertise, and please accept my apologies for reviving an older thread. Best regards, Martín

Link to this post | posted 29 Jun, 2025 15:13
scaruso	Kristen and Lee, We have struggled on using DNAM, but I think its day's are numbered. So if you whether it is a formal or informal outline of how you use it, I would be very happy to see what you are doing as I plan for this upcomming winter and the following spring. Thanks! Steve

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 03 Jul, 2025 20:47
mespariz	Lee, Thank you for sharing these valuable resources and your workflow details. The tutorials and Qubeshub materials will be very useful for our annotation process. I appreciate you outlining your training approach, it provides excellent guidance as we develop our own. I may follow up with a few questions as we try to implement them. Best regards, Martín

Link to this post | posted 03 Jul, 2025 21:07
scaruso	Lee, That is super helpful. I use PECAAN all the time, but haven't had to figure out how to use it in a class setting yet, so I am really looking forward to seeing how you went about it. Thanks again! Steve

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