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Recent Activity
JustinA posted in Plaques appear on spot test, don't appear in titer
Viknesh Sivanathan posted in Plaques appear on spot test, don't appear in titer
JustinA posted in Plaques appear on spot test, don't appear in titer
Viknesh Sivanathan posted in Plaques appear on spot test, don't appear in titer
RyanWheeler posted in Plaques appear on spot test, don't appear in titer
All posts created by debbie
| Link to this post | posted 31 Jul, 2023 14:22 | |
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Kathleen, Yep. debbie |
Posted in: Functional Annotation → WhiB family transcription factors
| Link to this post | posted 11 Jul, 2023 18:17 | |
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Hi! The server is down. Please refer to this post for updates. https://seaphages.org/forums/topic/5569/ |
Posted in: DNA Master → DNA master server down?
| Link to this post | posted 11 Jul, 2023 18:15 | |
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Liz, i just inquired today. It is still not available. debbie |
Posted in: Bioinformatic Tools and Analyses → DNA Master not updating
| Link to this post | posted 29 Jun, 2023 01:49 | |
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Hi all, Still working on it. Likely will not be available until the week of July 9. if you are a SEA-PHAGES faculty member and if you have an URGENT needed for a very tricky workaround, contact Kristen Butela KAB340@pitt.edu. There are no new updates to DNA Master (last build is 2705, but even 2701 will work), so they can ignore update errors. Their programs will work just fine without any need to update for the time being. If people are just getting the update error on existing installs, then they should just turn off automatic updates for now. Only faculty who need a fresh installation need to contact Kristen for a manual update. debbie |
Posted in: Bioinformatic Tools and Analyses → DNA Master not updating
| Link to this post | posted 28 Jun, 2023 20:17 | |
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Hi Marie, I agree,141 is Hypothetical Protein for now and you can assign ADP-ribosyltransferase to 142. interesting, GeneMark seems to include the preceding gene in a frameshift like thing….. (not that we are calling any of that…  Thanks for including the data. debbie |
| Link to this post | posted 21 Jun, 2023 19:03 | |
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Sally Molloy (University of Maine, Honors College) has shown an in-depth investigation of what is needed to call a protein RecA. Attached is a doc with links to her Power Point presentation and her video describing her presentation. |
12KbPosted in: SMART Function Investigations → RecA requirements
| Link to this post | posted 21 Jun, 2023 18:36 | |
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Maria, Thanks for sharing this. i hope others find it helpful. best, debbie |
Posted in: Phage Discovery/Isolation → Electron Microscopes
| Link to this post | posted 16 Jun, 2023 14:30 | |
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If you are unsure of how to call the sigma factor, we recommend not calling it as such, instead use DNA binding protein. |
| Link to this post | posted 16 Jun, 2023 12:41 | |
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Cluster A phages can have tyrosine, serine integrases, or partitioning genes. For the serine integrates, see the note about Bxb1 starts. Serine recombinases are called jumbo integrases because their size hovers around 500 amino acids (can go up over 700 amino acids). Look for serine residues in the N-terminus. Historically we didn't differentiate serine integrases from tyrosine integrases. Ask for help if you can't tell which one is in your genome. Some Cluster A phages, (I believe the first one identified is RedRock) don't have an integrase, but exist as an extra-chromosomal inhabitant of a bacterial cell. In order to be propagated, a partitioning system is utilized. See this paper for details: Dedrick RM, Mavrich TN, Ng WL, Cervantes Reyes JC, Olm MR, Rush RE, Jacobs-Sera D, Russell DA, Hatfull GF. Function, expression, specificity, diversity and incompatibility of actinobacteriophage parABS systems. Mol Microbiol. 2016 Aug;101(4):625-44. doi: 10.1111/mmi.13414. Epub 2016 Jun 10. PMID: 27146086; PMCID: PMC4998052. |
Posted in: Cluster A Annotation Tips → Integrases/Partitioning Systems
| Link to this post | posted 15 Jun, 2023 02:50 | |
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The F2 phage Soul22 was annotated with a single immunity repressor but at the time we were annotating the genome, we did find another gp that we could have called an immunity repressor, but it more resembled that in A1 phages. So we did not identify the function as an immunity repressor. But it may very well be an immunity repressor but NOT to the F2 phages but to A1 phages (I have some prelim lab data indicating it is functional as one against A1 phages; we will be following up on this in the fall). The A1 repressor is also found in at least some C1 phages. Bottom line – how do we annotate a second immunity repressor that is specific for a different cluster than the phage it is found in? This post and question was constructed at 2023 Faculty Meeting: Cluster Specific Annotation Tips. Hi all, This is definitely worth the post, but more data is needed to annotated this. When wet bench data is available, post here. We are looking forward to those experiments! debbie |