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Recent Activity
All posts created by debbie
| Link to this post | posted 03 Aug, 2023 20:20 | |
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Hi Steve, Will you record? Thanks, debbie |
Posted in: General Message Board → Observable Office Hours
| Link to this post | posted 31 Jul, 2023 19:31 | |
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The approved function list says you have to have a transposon to have a transposase. I don’t know the answer to that. I would ask that you looks as well as you can and if you don’t find something that looks like a transposon, just call the transposase and make note on your cover sheet. Another thing to consider is the types of transposons – papers will define the ends and that may help you find the transposon. |
Posted in: Functional Annotation → Identify transposons
| 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. |