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Recent Activity
cdshaffer posted in Whole phage starterator reports
fbaliraine posted in Phage DoRead Start at 52714 bp with 8 bp overlap vs start at 52718 with 4 bp overlap?
Debbie Jacobs-Sera posted in Phage DoRead Start at 52714 bp with 8 bp overlap vs start at 52718 with 4 bp overlap?
All posts created by debbie
| Link to this post | posted 16 Mar, 2024 22:16 | |
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From Ann Findley: "I just checked with our computer science folks who were responsible for writing the code and administering the database. Unfortunately, when they went into the AWS account that was hosting the PET they were not able to recover the code. The latest information is that they are attempting to use an earlier version of PET to resurrect the tool. I am not certain of their timeline for completion." Best, debbie |
Posted in: General Message Board → Phage Enzyme Tools - PET2.0 - Down?
| 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 |
Posted in: DNA Master → Critical Update: Installing New Copies of DNA Master or Updating Old Versions of DNA Master prior to Version 2701
| 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 |
Posted in: Cluster F Annotation Tips → 4 bp overlaps
| 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 |
Posted in: Cluster EE Annotation Tips → Genome Curation - a must read!
| 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 |
Posted in: Gene or not a Gene → Is the current subcluster A4 pham 4236 (as of 2/14/2024) really a gene?
| 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 |
Posted in: Cluster FC Annotation Tips → Annotated Cluster FC Phages
| 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 |
Posted in: Choosing Start Sites → Two consecutive ATG start sites