Link to this post | posted 08 Jan, 2026 01:12

debbie

Hi Beth, I'm finally answering this here also. Sorry for the delay. The original University of Pittsburgh server that housed DNA Master is no longer available. User the directions in the Genomics guide, section 2.5 to get DNA master installed. do not use any previous directions. And do not auto-install. Change the location of installation as described in the guide. And for those of you who are struggling with this installation. DNA Master provides information that is essential for a good annotation. IN a classroom setting, pair up your students, then you only need 1/2 as many computers loaded with this software! there is plaenty of work to do with the other programs. Best, debbie

Link to this post | posted 04 Jan, 2026 23:20
debbie	Steve, We should be back on a Friday schedule, so anticipate January 9, 2026. bBst, debbie

Link to this post | posted 29 Dec, 2025 22:05
debbie	Yes! That is the appropriate message because the "G" and the "G/T" genes of the tail assembly chaperone pair do a share the same start! Check out the paper listed in the Genomics Guide! debbie

Link to this post | posted 29 Dec, 2025 20:20

debbie

Hi all, Directions for annotating a programmed frameshift are found here. https://genomicsguide.seaphages.org/ What Lee has said is all true, but doesn't apply to this particular frameshift because you have a +1 frameshift and Lee has described a -1 frameshift. This video describes how to annotate a +1 frameshift. It happens to be very similar to the frameshift in Vivum. https://seaphages.org/video/79/ The 2 regions of the programmed frameshift of the tail assembly chaperone gene of Vivum are 8539-9036, 9038-9475. Let me know if you have any questions. debbie

Link to this post | posted 18 Dec, 2025 22:00
debbie	Chris, Thanks to you and your IT for the quick response to this request! debbie

Link to this post | posted 17 Dec, 2025 00:58

debbie

Hi all, When Starterator posts a note that "Report not found", the most likely explanation is that it is updating. Please first wait a bit before asking for help. (Typical updating time is ~4 hours.) In addition, servers, like Chrome, are starting to deny/limit access to http sites. Chris Shaffer will be getting starterator on an https site soon. In the meantime try a different server. December 16, 2025 Thanks, debbie Edited 17 Dec, 2025 01:13

Link to this post | posted 16 Dec, 2025 05:14
debbie	Hi all, After careful review at the 2025 Genomics Workshop with Graham's help, the correct call for terminase, small subunit is gene 3 (in Toad24). The hits to Pfam database are equally convincing for gene 3 and gene 58. Gene 3 is in the canonical place.

Link to this post | posted 10 Dec, 2025 14:44
debbie	Jaya, Of course! What you put on the plate is what the yield will be. Best, debbie

Link to this post | posted 10 Dec, 2025 01:54
debbie	For 2025 Genomics Workshop, Lindsay Constantini (from NCCU), was able to get a DNA Master installation to work on Crossover. Attached are the ChatGTP steps and some troubleshooting she used to install via Crossover on her MacOS. best, debbie 30Kb

Link to this post | posted 08 Dec, 2025 19:10

debbie

HI all, I think that the answer is in this post above. Please read above. In general, the 2 genes of terminase do different things. It is a good time to check the literature on this. There are many articles that articulate what these genes do. Here is an article that describes a non-canonical display of the Terminase, large subunits parts. Zhao H, Christensen TE, Kamau YN, Tang L. Structures of the phage Sf6 large terminase provide new insights into DNA translocation and cleavage. Proceedings of the National Academy of Sciences of the United States of America. 2013;110(20):8075-8080. doi:10.1073/pnas.1301133110. The small terminase is more elusive, and sometimes we cannot find it. It can also be part of the large terminase gene. debbie