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Recent Activity
All posts created by debbie
| 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 |
| Link to this post | posted 20 Jul, 2021 14:44 | |
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Hi Fred, I HHPred'd Mach genes 5,6,7 (as found on phamerator). I would call all 3 as minor tail proteins. I used these 4 databases to search: PDB, PfamA, CDD, and Uni-Prot-Swiss Protein-viral. I did not use Scope. Because you are calling structural genes in cluster A, A2 in particular, I would want to be sure to not overwrite any historical data (that would include some bench work) that has been derived about well studied phages such as D29. When you include the HHPred results from the Uni-Prot database, you have significant hits to minor tail proteins. In addition, when you phamerator MaCh and Duplo together, gene 7 of MaCh hits gene 34 of Duplo, a much more canonical orientation for a minor tail protein. See what you think! debbie |
| Link to this post | posted 20 Jul, 2021 14:07 | |
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Hi. I think that this forum post will help. https://seaphages.org/forums/post/8693/ Let me know, debbie |
Posted in: DNA Master → FTP Error on Windows 10 Pro