SEA-PHAGES | All posts created by debbie

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Link to this post \| posted 02 May, 2023 12:52
debbie	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 12:52

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

Posted in: Cluster A Annotation Tips → Lysins A and B not following synteny

Link to this post \| posted 02 May, 2023 12:36
debbie	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 02 May, 2023 12:36

debbie

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

Posted in: tRNAs → Follow-up Clarifying Question about tRNA and protein genes not overlapping

Link to this post \| posted 01 May, 2023 17:45
debbie	Thanks!

Posted in: DNA Master → Function field

Link to this post \| posted 01 May, 2023 12:56
debbie	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

Posted in: DNA Master → Function field

Link to this post \| posted 01 May, 2023 12:51
debbie	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

Posted in: How to Pass Preliminary Annotation Review → How to Pass Preliminary Annotation Review

Link to this post \| posted 01 May, 2023 12:48
debbie	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

Posted in: DNA Master → DNAMaster BLAST failure

Link to this post \| posted 27 Apr, 2023 15:43
debbie	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

Posted in: Gene or not a Gene → Gene or no gene?

Link to this post \| posted 26 Apr, 2023 20:29
debbie	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

Posted in: tRNAs → Trimming a tRNA only called by tRNA scan-SE

Link to this post \| posted 23 Apr, 2023 23:58
debbie	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 87Kb

Link to this post | posted 23 Apr, 2023 23:58

debbie

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

Posted in: Cluster F Annotation Tips → 4 bp overlaps

Link to this post \| posted 19 Apr, 2023 23:55
debbie	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

Posted in: Annotation → 5’nucleotidase v. phosphatase

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All posts created by debbie