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Recent Activity
All posts created by debbie
| Link to this post | posted 18 Jun, 2024 01:34 | |
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Hi Amanda, What do you consider a jumbo phage? thanks, debbie |
Posted in: General Message Board → Jumbo phage annotation
| Link to this post | posted 04 Jun, 2024 01:51 | |
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Hi all, GenBank has been re-writing the lineage submission lines for quite a while now. There are 2 issues with what they are doing. First, their records are incomplete. The number of phages that we keep entering is difficult to keep up with, so sometimes they don't offer much. Secondly, we don't really ascribe to this lineage and have found that offering a classification of siphovirus, myovirus, or podovirus may be more helpful. Regardless of what write, they overwrite it. Step carefully as you wade into this to get your MRA published. best, debbie |
| Link to this post | posted 23 May, 2024 20:28 | |
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Hi Shallee, Rick Pollenz is looking at transmembrane proteins associated with the lysin genes. He may have more insight. Though I am not an expert, it is my understanding that our lysin Bs 'contain' the analogous spanin function of the enteric bacteriophages. So we have avoided using 'spanin' in lieu of lysin B. with the difference in cell walls we would want to be careful that are calls do not cause confusion. You are welcome to deep dive this topic! debbie |
Posted in: SMART Function Investigations → spanins
| Link to this post | posted 21 May, 2024 21:34 | |
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Ping, I can verify that it is down. If it isn't back by tomorrow, i will contact the folks at GeneMark. debbie |
Posted in: PECAAN → GeneMarkS ?
| Link to this post | posted 15 May, 2024 23:13 | |
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Hi Dane, From the HHPred results, because of the limited nature of the hits, i would not call anything at this time. best, debbie |
Posted in: Annotation → capsid maturation protease or hypothetical protein (MuF-like minor capsid protein)
| Link to this post | posted 10 May, 2024 01:15 | |
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Alison and your students, Thank you for your awesome work on this. Maria Gainey presented this and her similar protein at our SMART meeting today and a discussion ensued. For now, we recommend that you call this protein "cyclic nucleotide inhibitor". best, debbie |
| Link to this post | posted 09 May, 2024 02:16 | |
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Hi Nikki, Sorry to id the paper as Tweety, when the data is about Fruitloop. Bit I di have the paper right! (Just what you needed, more confusion.) I think your decision is a good as we can get at this point. best, debbie |
Posted in: Gene or not a Gene → F1 cluster forward reverse or neither?
| Link to this post | posted 03 May, 2024 18:42 | |
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Be careful what you say about Fruitloop. Go to the paper and see the mas spec table and the map there. (when I looked, the paper doesn't match the GB file). There is a gene in there that you do want to call. i just don't have time right now to match it correctly. Let's touch base before you submit. best, debbie |
Posted in: Gene or not a Gene → F1 cluster forward reverse or neither?
| Link to this post | posted 03 May, 2024 16:20 | |
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Hi Nikki, Mycobacteriophage Tweety has a paper that includes mass spec data. While the integrase and repressor have less sequence homology, that space in between may have enough similarity that you can draw some inferences that are applicable. Let me know what you think. https://onlinelibrary.wiley.com/doi/full/10.1111/mmi.13946 Best, debbie |
Posted in: Gene or not a Gene → F1 cluster forward reverse or neither?
| Link to this post | posted 24 Apr, 2024 19:04 | |
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You are welcome! debbie |
Posted in: Cluster CS Annotation Tips → CS2 Holin Gene