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Recent Activity
cdshaffer posted in Whole phage starterator reports
fbaliraine posted in Phage DoRead Start at 52714 bp with 8 bp overlap vs start at 52718 with 4 bp overlap?
Debbie Jacobs-Sera posted in Phage DoRead Start at 52714 bp with 8 bp overlap vs start at 52718 with 4 bp overlap?
All posts created by debbie
| Link to this post | posted 17 Jan, 2025 17:22 | |
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Iain, Refer back to the installation guide https://phagesdb.org/DNAMaster/ and see if the Chromo Book has the right specs. I am guessing that it does not. But check and see! Best, debbie |
Posted in: DNA Master → DNA Master and Chromebook
| Link to this post | posted 13 Jan, 2025 19:09 | |
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Hi all, the most likely reason that you are not updating is that you are not running as an administrator. If IT is doing it, they will have privilege. If you are doing it, DON'T install in Program files, instead install elsewhere, like the desktop. Right click on the program, run as administrator to complete the update. debbie |
Posted in: DNA Master → Critical Update: Installing New Copies of DNA Master or Updating Old Versions of DNA Master prior to Version 2701
| Link to this post | posted 13 Jan, 2025 18:53 | |
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Kristen and Liz, Not that I am aware. The latest cohort just installed for the December workshop. Updating, as long as the preferences were set correctly, was not an issue. debbie |
Posted in: DNA Master → Critical Update: Installing New Copies of DNA Master or Updating Old Versions of DNA Master prior to Version 2701
| Link to this post | posted 09 Jan, 2025 02:56 | |
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Cool paper about the tRNA expressed in the prophage (Fionnbharth) in M. smegmatis mc2. 155. https://journals.asm.org/doi/10.1128/mbio.03260-23 It is a VERY atypical bench determined expression of a tRNA. |
| Link to this post | posted 26 Dec, 2024 17:19 | |
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I would pick the latter, so the slippage is annotated as 10569-11030, 11030-11464. This slippage matches the programmed frameshift of phage Lambda, which is the phage where the slippage was experimentally determined. https://pubmed.ncbi.nlm.nih.gov/8230192/ best, debbie |
Posted in: Cluster C Annotation Tips → frameshift
| Link to this post | posted 20 Dec, 2024 03:42 | |
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Christine, With no experimental evidence, it is difficult to say which it is, but it is thought that the +1 frameshift is far more common than the -2. So that is what I would annotate. There are a lot of unannotated frameshifts in this subcluster, mostly becsuse we made a decision to only annotate those sequences found in the literature. (See the guide for the list). However, this sequence is so well conserved, i think it can be called. debbie |
Posted in: Cluster L Annotation Tips → L3 frameshift
| Link to this post | posted 16 Oct, 2024 13:00 | |
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Excellent! |
Posted in: Arthrobacter → Arthrobacter vanishing plaques
| Link to this post | posted 11 Oct, 2024 14:01 | |
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Terrific! You can do this! debbie |
Posted in: Arthrobacter → Arthrobacter vanishing plaques
| Link to this post | posted 11 Oct, 2024 13:39 | |
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Hi Colleen, The simplest answer is that you are not propagating A. globi any longer. Do you have your original stock material? It is time to revert to that! A good practice is that all cultures be subbed from the parental strain, an F1 or F2 generation is fine, but going beyond that is problematic. Best, debbie |
Posted in: Arthrobacter → Arthrobacter vanishing plaques
| Link to this post | posted 10 Oct, 2024 14:32 | |
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Hi Colleen, Does the control phage provide show no plaques also? debbie |
Posted in: Arthrobacter → Arthrobacter vanishing plaques