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Recent Activity
Debbie Jacobs-Sera posted in what on earth is this thing (TEM)
nic.vega posted in what on earth is this thing (TEM)
cdshaffer posted in 260/280 ratios too high from DNA extraction
Viknesh Sivanathan posted in 260/280 ratios too high from DNA extraction
Viknesh Sivanathan posted in 260/280 ratios too high from DNA extraction
All posts created by debbie
| Link to this post | posted 23 May, 2025 22:23 | |
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Kurt, This could be a bunch of things. My first guess is the actual files that you are comparing. Do the genomes open in DNA Master? It is likely a corrupt file I think. debbie |
Posted in: DNA Master → Genome Comparison
| Link to this post | posted 16 May, 2025 17:51 | |
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Noe, look at line 65 in the approved function list (directly below the crossed out item). that hit is called a nuclease domain in the databases we use, but there is no nuclease function to that sequence. it is now named "ParB N-terminal-like domain" debbie |
Posted in: Cluster C Annotation Tips → ParB-like nuclease domain
| Link to this post | posted 13 May, 2025 15:06 | |
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Chris and Maria, Excellent choices! Only call one. And do not call a wrap round version. debbie |
| Link to this post | posted 06 May, 2025 17:36 | |
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Aurturo, Please use PineapplePizza as your prototype as to what to call each tail type in your pododvirus. I used P68 and phi29 as the prototypes to call that one. For genes 17 and 18 of Smelly (phamerator_draft), you can call both as minor tail proteins. Once you do that, If you have any questions, continue on the forum post. Thanks, debbie |
| Link to this post | posted 05 May, 2025 15:19 | |
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Nikki, The data is coming fast and furious. For now, I would call these Hypothetical Proteins. but soon, we may have a better understanding. Best, debbie |
| Link to this post | posted 01 May, 2025 23:28 | |
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Hi all, When annotating a Cluster O paper, please refer to this paper for help "Comparative Genomics of Cluster O Mycobacteriophages" https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0118725 |
Posted in: Cluster O Annotation Tips → Cluster O paper
| Link to this post | posted 01 May, 2025 23:19 | |
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Iain, Did you have a working DNA master? If not use this forum post to install. https://seaphages.org/forums/topic/5577/ If you did have a working copy, it has not been updated since Oct 24, 2021. The server where it sat is no more. So there is no need to update and you can't because the server is not available any more. We are working on it. The link above does work. debbie |
Posted in: DNA Master → Issue uninstalling DNA Master
| Link to this post | posted 01 May, 2025 16:40 | |
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Arturo, Sure that will work. It would also be appropriate to call it a "endolysin, protease M15 domain". (I like this one better because it is less letters. debbie |
Posted in: Functional Annotation → Two endolysins?
| Link to this post | posted 21 Apr, 2025 23:34 | |
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tRNA Scan SE may be back up, but it is still not showing the pictures. Please check the structure of the tRNAs if not available in tRNA Aragorn. Thanks, debbie |
Posted in: Bioinformatic Tools and Analyses → tRNAscan-SE
| Link to this post | posted 16 Apr, 2025 19:28 | |
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We won't merge the products. But I think it is reasonable to say they are the parts of whole. Bench data to support this would be great! I don't always call this, but in this case, I think it is a reasonable call. debbie |