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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 07 Mar, 2024 15:58 | |
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Hi Katie and Steve, The space where the DNA Master server lives is undergoing renovations. It is expected to be back next week. I'll keep you posted. debbie |
Link to this post | posted 03 Mar, 2024 20:46 | |
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Fred, I wold not look to fill this space in the same way I might be inclined to do so at the right end of the genome. This space is likely part of the immunity cassette, and is likely expressed during lysogeny. I would not call this gene. debbie |
Link to this post | posted 03 Mar, 2024 11:03 | |
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Thank Claire, After reviewing your data, i am beginning to believe that conformity is not all that its cracked up to be! I agree with your assessment of gene 18 in Luxx. the 4-base overlap is much more convincing than the bigger overlap. We used alpha-fold to fold the longer version of 18 and the lysin, and no structures were observed to be helpful. So while the data may not change for a while, I agree that the start choice that Claire points out (the 4 base overlap) is a better choice. For genes 21 and 22, I like the original 'conformity' calls because of coding potential evaluations. So call upon your best gene evaluation skills and make your best call. Please draw attention to these genes in your cover letter, so that the QCer can also evaluate. Anyone want to do some bench work?!! Best, debbie |
Link to this post | posted 29 Feb, 2024 02:40 | |
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Check HHPred results. Yes, they are not in the typical synteny. Though it is not common, it is not uncommon. debbie |
Link to this post | posted 22 Feb, 2024 21:48 | |
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I changed the approve function to say: "Typically has HEXXH motif but other metalloprotease motifs (e.g. "ExnHxHx7Sx2D)" debbie |
Link to this post | posted 21 Feb, 2024 18:20 | |
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Hi Beth, What phage are you annotating? Could you provide the phamerator gene number and its stop codon. Thanks, debbie |
Link to this post | posted 17 Feb, 2024 13:54 | |
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Fred, I think you have a good choice! Best, debbie |
Link to this post | posted 16 Feb, 2024 17:06 | |
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H John, This is on my plate to fix. They will be in phamerator soon debbie |
Link to this post | posted 15 Feb, 2024 20:12 | |
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I don't think that it matters if they are ATG, GTG, or TTG. Starts are starts and the amino acids chain start with an fMet. debbie |
Link to this post | posted 15 Feb, 2024 15:17 | |
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Hi Fred, The right arm of some of our well studied mycobacteriophages defy common annotation practice. Here is how I look at it. We have published papers where the right arm has no coding regions because there are RNAs expressed. The paper about mycobacteriophage Giles has the best display of bench data that we have. I am always cautious to not overcall the right end of a genome. I think these are some of the stats to consider: This ORF is only found in Cluster A4s. Phamerator has it as 17/134 genes annotated. Are they all drafts? How many of them have the nucleotide sequence? How conserved is it? Could it be something other than a protein coding sequence? You mention no coding potential. Nor, is it easy to see how this gene would get easily made. Check out other cluster A phages like L5 or D29 and note they are not over-calling this region. Also, what is the risk if you delete it? Do you think a researcher who want to investigate lemur_85 isn't going to find this segment of DNA in Alberto7. Most important is that you can support whichever call that you make. Looking at all of the data is and not what others have done will get you to a best answer. Good luck as you make this decision! debbie |