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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 02 May, 2023 12:52 | |
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Kathleen and students, I would say your phage is canonical for a Cluster A3 phage, and the lysins are where they are and, I guess, where they are supposed to be. And the holin is elusive. I just QUICKLY looked at the proteins with transmembrane and HHPredded gene 30 of BlueBird. It has 2 transmembrane proteins and is located at the end of the minor tail proteins. It has a non-significant hit to a holin. Though I don't reccomened calling it, I would bet a nickel that it is indeed the holin. debbie |
Link to this post | posted 02 May, 2023 12:36 | |
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Hi Fred, I think that you have covered all of the bases in this evaluation. I would avoid calling this gene. The instances where I know there is a tRNA in a predicted protein do not look like this one. However, when I saw the hit to an HNH that was confounding. However, I don't think it is an HNH. The H-N-H seems missing to me. I would call call the protein, but include the tRNAs. I would also draw attention to this in your cover sheet. The QCer will review all of this to confirm. Best, debbie |
Link to this post | posted 01 May, 2023 17:45 | |
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Thanks! |
Link to this post | posted 01 May, 2023 12:56 | |
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Joe and Katie, I am not following this, so I am going to restate. Some people use the function field as a holding area when working in DNA Master. The final minimal file should have nothing in the function field. (All functions are recorded in the Product filed.) In fact, it is good to use the "clear all" buttons in DNA Master to be sure there are no stray characters there. debbie |
Link to this post | posted 01 May, 2023 12:51 | |
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Hi Pam, You can submit Hypothetical Protein as Hypothetical Protein or hypothetical protein. The capitalization is related to how it is automated in DNA Master and PECAAN, respectively. Sorry that is confounding, but it is the small stuff. Best, debbie |
Link to this post | posted 01 May, 2023 12:48 | |
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Katie, I can confirm that that happens. (But I am not recalling the reasons.) Just note what didn't blast on your cover sheet and submit. All good! debbie |
Link to this post | posted 27 Apr, 2023 15:43 | |
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Hi Ellen, I do not see any coding potential in this area. I would not call a gene there. Also remember that the red dotted lines of coding potential are not a good indicator of coding potential. (The represent patterns of 2 nucleotides (which is very noisy). best, debbie |
Link to this post | posted 26 Apr, 2023 20:29 | |
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Ellen, I agree with your decision of where to cut. Well done! It is not a very pretty tRNA, but I think it should be called. debbie |
Link to this post | posted 23 Apr, 2023 23:58 | |
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Hi! AlpineSix's programmed frame shift has to be a +1. Check out the relationship of the "G" gene to the "T" gene. It does not appear to have a canoninical frameshift, BUT was called by the researcher who did the research on frameshifts, so we will do the same. Check out the frame-shift in Che8. I have attached a photo of the DNA Master annotation of AlpineSix. Let me know if you have any further questions. debbie |
Link to this post | posted 19 Apr, 2023 23:55 | |
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Lee, glad it makes sense. it is not that the 5'nucleotidase could be correct, we just don't know enough to be that specific…..yet. debbie |