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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 17 Jul, 2024 02:20 | |
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A function is now listed on the approved function list with a link to this entry. thank you! debbie |
Link to this post | posted 09 Jul, 2024 14:32 | |
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Maria, What gene is your example? I'll add this to the approved function list! debbie |
Link to this post | posted 08 Jul, 2024 19:22 | |
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Hi all, Be extremely cautious with using NCBI Blast hits for anything right now. Their Ref_Seq data is at the very least problematic and at its worst is just plain wrong. With our data set being so great, and if you only post 100 hits, using NCBI for anything yields nothing of value over a phagesDB blast because it will only hit our data. If you are not hitting our data, tread just as cautiously because that data may/may not be hand curated. Which means you could be comparing your data to raw Glimmer/GeneMark data with no personal evaluation. So it would not be very helpful. There are many cases in our forums where folks have hit Ref_Seq information that is incorrect. 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 |
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 |
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 |
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 |
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 |