Link to this post | posted 20 Feb, 2025 15:52
lhughes	Hmmm - I don't see anything wrong there. The screenshot doesn't show the bottom of the page, but does it show the two regions as bars? As well, does your description page for the gene have the correct start/stop for the longer product, as well as "2" in the regions box? It seems odd that the "incorrect" notice doesn't show any coordinates, just zeroes. I wish I was able to be more helpful! Lee

Link to this post | posted 19 Feb, 2025 18:37
lhughes	Can you show what's on the "Regions" tab for the gene? I'm guessing that the lengths for each region are possibly not correct there. 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

Link to this post | posted 12 Jan, 2024 21:09
lhughes	Congratulations on your retirement, David! It has been wonderful to have the opportunity to interact with you as the SEA has grown. Thank you for all you have done to help make this possible. All the best, Lee Hughes

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 07 Jun, 2023 16:53
lhughes	Kathleen, Did you ever get an answer to this question? We just got sequence back on a new BM and will be annotating it in the near future, so I am interested in what you found out. If you haven't gotten an answer yet, it might be worth emailing Chris Shaffer for more information. Lee

Link to this post | posted 09 May, 2023 13:46
lhughes	Thanks, Debbie. Good to know it's not just me, and thanks for the thoughts on a workaround. Lee