Link to this post | posted 17 Sep, 2021 16:24
debbie	Hi all, My last posts were misguided. It was the license problem. GeneMark is back on line! debbie

Link to this post | posted 16 Sep, 2021 21:12
debbie	I just talked to Christian and he suggested the simplest explanation is the Preference Settings in the Secure Connections panel are not set properly. See the attached picture for what they should look like. Going forward, would you let me know if you still have problems what DNA master build number you are using. (The latest build that i have is 2704.) Thanks! 164Kb

Link to this post | posted 16 Sep, 2021 21:04

debbie

Good info. I have no idea if this will have any impact. The latest 'fix' is about active and passive FTP. Make sure that in your preferences -> Internet setting ->Home Site that you match the setting that I have. (This is the only preference i have modified lately.) And as another data point, I auto-annotated a new to me genome this morning and DID get GeneMark data in my auto-annotation. debbie 143Kb

Link to this post | posted 16 Sep, 2021 00:25
debbie	Kathleen, Here is the next thing that I would like you to check/try. Check out your auto-annotation choices. Do you have both analyses checked as int he attached photo? Thanks, debbie Edited 16 Sep, 2021 00:29 113Kb

Link to this post | posted 15 Sep, 2021 21:34

debbie

Hi Kathleen, Would you try again? I just auto-annotated a genome and got GeneMark results. The license to use GeneMark's server seems to be dependent on use, so it is not easy to predict when we have to update it. It could have just been updated after you auto-annotated. If that is true then you will get GeneMark results when you repeat. If you don't get GeneMark results when you repeat, I am not sure what the problem is and will investigate further. Keep me posted, debbie

Link to this post | posted 31 Aug, 2021 02:11
debbie	Hi all. Kristen is correct. We are aware of this issue and are working on it. debbie

Link to this post | posted 20 Aug, 2021 15:44
debbie	Yes. I think so.

Link to this post | posted 20 Aug, 2021 14:56
debbie	Hi! I think that this is the issue: If the 'Use PBI server…" is not on your screen, you still need to update DNA Master to continue. Be sure to update as an administer. debbie

Link to this post | posted 04 Aug, 2021 19:04
debbie	In addition to the terminase, large subunit in cluster J phages, they contain another gene (gp3 in Omega) that hits the N-terminus of terminase. Please refer to the Cluster J paper for further explanation of this gene call. https://pubmed.ncbi.nlm.nih.gov/23874930/

Link to this post | posted 28 Jul, 2021 01:22
debbie	Hi Arturo, Sorry for the delay on this one. One of the hits is with HK97_gp10. This phage was well studied in the Hendrix lab here at Pitt, and they are have studied capsid proteins in depth. They could not determine what its function was, so I would not call it a minor capsid protein, and stick with Hypothetical Protein for now. debbie