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Recent Activity
All posts created by debbie
| Link to this post | posted 16 Sep, 2021 21:04 | |
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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 |
143KbPosted in: DNA Master → Auto-annotation fix for fall 2017 and later
| Link to this post | posted 16 Sep, 2021 00:25 | |
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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 |
113KbPosted in: DNA Master → Auto-annotation fix for fall 2017 and later
| Link to this post | posted 15 Sep, 2021 21:34 | |
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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 |
Posted in: DNA Master → Auto-annotation fix for fall 2017 and later
| Link to this post | posted 31 Aug, 2021 02:11 | |
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Hi all. Kristen is correct. We are aware of this issue and are working on it. debbie |
Posted in: DNA Master → DNA Master Issue
| Link to this post | posted 20 Aug, 2021 15:44 | |
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Yes. I think so. |
Posted in: DNA Master → DNA Master Issue
| Link to this post | posted 20 Aug, 2021 14:56 | |
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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 |
Posted in: DNA Master → DNA Master Issue
| Link to this post | posted 04 Aug, 2021 19:04 | |
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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/ |
Posted in: Cluster J Annotation Tips → Terminase? gene
| Link to this post | posted 28 Jul, 2021 01:22 | |
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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 |
Posted in: Cluster EJ Annotation Tips → Potential minor capsid protein
| Link to this post | posted 25 Jul, 2021 16:39 | |
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Hi Susan, You will likely have to delete the project and start again. Does DNA master let you do that? debbie |
Posted in: DNA Master → Error flushing tables
| Link to this post | posted 21 Jul, 2021 22:38 | |
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Fred, I am just learning about the Uni-Prot-Swiss Protein database, and all data there is not the same. I don't think i have had any significant data reported from Scope, which is why i started using Uni-Prot. I feel like i am beta testing it for now. Try it out and see what you find! debbie |