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Recent Activity
byrumc@cofc.edu posted in Getting Started with Phage Assembly
byrumc@cofc.edu posted in Getting Started with Phage Assembly
byrumc@cofc.edu posted in Getting Started with Phage Assembly
byrumc@cofc.edu posted in Classificiation with ICTV guidelines
Debbie Jacobs-Sera posted in Classificiation with ICTV guidelines
All posts created by debbie
| Link to this post | posted 07 Dec, 2022 16:11 | |
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Working on Microbacterium phage Jefe at the 2022 Genomics Workshop! It is one of the members of this cluster where no slippery sequence can be identified. The upstream gene of the TAC pair has a Pfam hit to tail assembly chaperone, so call it. However, there is no data to support a tail assembly chaperone call for the second gene, NOR its there a slippery sequence present. that gene is a Hypothetical Protein. |
| Link to this post | posted 23 Nov, 2022 14:52 | |
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Hi Nikki, I think the Starterator picture shows that the 25523 is a best call. You can see it line up across different clusters/subclusters. I would call 25523. debbie |
| Link to this post | posted 18 Nov, 2022 02:45 | |
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Cluster GC genomes may have 2 capsid proteins. See the note at Cluster DC. https://seaphages.org/forums/topic/5430/?page=1#post-9831 |
Posted in: Cluster GC Annotation tips → 2 major capsid proteins
| Link to this post | posted 18 Nov, 2022 02:43 | |
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Cluster DE5 genomes may have 2 capsid proteins. See the note at Cluster DC. https://seaphages.org/forums/topic/5430/?page=1#post-9831 |
Posted in: Cluster DE Annotation Tips → 2 major capsid proteins
| Link to this post | posted 18 Nov, 2022 02:40 | |
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Cluster EC genomes may have 2 capsid proteins. See the note at Cluster DC. https://seaphages.org/forums/topic/5430/?page=1#post-9831 |
Posted in: Cluster EC Annotation Tips → 2 major capsid proteins
| Link to this post | posted 18 Nov, 2022 02:35 | |
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Simon White's CroEM work has discovered that the major capsid in some of our genomes is made with 2 genes - a major capsid pentamer protein and a major capsid hexamer protein in Rosebush (Cluster B2). Cluster DC genome have the same hexamer protein and a homolog of the pentamer protein. Examples are: Wizard gp 19 - major capsid hexamer protein Wizard gp 20 - major capsid pentamer protein |
2.94MbPosted in: Cluster DC Annotation Tips → 2 major capsid proteins
| Link to this post | posted 14 Nov, 2022 16:55 | |
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I think that this is a thymidylate kinase. |
| Link to this post | posted 11 Nov, 2022 03:00 | |
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Louise, Here is what has worked in the past. See if it still works. debbie https://seaphages.org/forums/topic/4795/ |
Posted in: DNA Master → DNA Master errors
| Link to this post | posted 04 Oct, 2022 16:37 | |
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If further info is needed, pictures would be helpful. Good luck! |
Posted in: Phage Biology → why is my agar green?
| Link to this post | posted 04 Oct, 2022 15:45 | |
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Hi Stephanie, If you are using 7H10 to make your agar, it contains malachite green and the agar should really be green. Once overcooked and autoclaved, it tends to be more tan than pale green. If this is the cause of the green, there is nothing wrong. If the agar is undercooked or autoclaved, it can appear greener, BUT you will also have no growth and/or contamination issues, which are a bigger problem. Does that fit what you are seeing? |
Posted in: Phage Biology → why is my agar green?