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Recent Activity
All posts created by debbie
Link to this post | posted 19 Jan, 2022 01:22 | |
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Chris, I am guessing that you do not have all of the preferences set correctly. In particular, make sure that #2 and 6 are correct. Let me know, debbie |
Posted in: DNA Master → Auto-annotation fix for fall 2017 and later
Link to this post | posted 14 Jan, 2022 22:44 | |
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Hi Kyle, The simple answer to you questions and assumptions is yes! The SMART Team is pretty smart and I think they will be able to follow whatever you provide. The purpose of these notes is 2-fold. One is help get to best answer in the genome review process. If you get to the best answer, they don't have to spend a lot of time in your notes. But, if they find the annotation lacking, the documentation of how you made the calls can help them. The second is to help you - the annotator - document your gene calls so that we can help where needed. We can't help you and you can't help you if you can't see the rationale of what you did. Don't over think this, make your notes meaningful and it will all work out. Check out the links posted above for more of the rationale. Sounds scary, but should simply. debbie |
Posted in: Notes and Final Files → Notes format when using DNA Master
Link to this post | posted 13 Jan, 2022 17:15 | |
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Hi Ann, In the words of Eeyore "Thanks for noticing!" The new direction is meant to make your decision making on your gene calling as simple as possible and as meaningful as possible. In addition, the notes were not very helpful in the QC process. I have modified 2 pages to help as you construct the notes that will work for you. https://seaphagesbioinformatics.helpdocsonline.com/article-44 https://seaphagesbioinformatics.helpdocsonline.com/officialdocumentation I am hoping that this post today will encourage others to upload "Here's what I use." The goal of this notes record is to provide the evidence needed to get annotations improved so that when you are done, they are really ready to go directly into GenBank. So asking for help or review along the way is encouraged. If you wish to use the same format for notes as before, that will be acceptable for now. Let me know if you have any questions. debbie |
Posted in: Notes and Final Files → Notes format when using DNA Master
Link to this post | posted 12 Jan, 2022 12:15 | |
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Sergei, GenBank has taken as little as 1 day and as much as 6 months to post genomes. I think it is best to just be patient and wait for the genome to post. Are you writing a MRA? debbie |
Posted in: Annotation → In Genbank
Link to this post | posted 05 Jan, 2022 21:06 | |
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Hi Rick, We will wait for the cryoEM, but yes, the must surely be the major capsid subunit. Nice! debbie June 21, 2022 Rick Pollenz and Simon White have confirmed (experimentally) that Akoni_gp33 is the major capsid subunit! Please annotate! |
Posted in: Cluster EK Annotation Tips → major capsid protein
Link to this post | posted 30 Dec, 2021 14:08 | |
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There are lots of papers to read when annotating a Cluster F phage. 3 specific papers to consider are: Comparative genomic analysis of mycobacteriophage Tweety: evolutionary insights and construction of compatible site -specific integation vectors for mycobacteria T.T. Pham et al, Microbiology 2007. Mycobacteriophage Fruitloop gp52 inactivatesWag31 (DivIVA) to prevent heterotypic superinfection C. Ko and G.F. Hatfull, Mol Micro 2018. An NAD+ Phopsphorylase Toxin Triggers Mycobacterium tuberculosis Cell Death D. M. Freire et al, Mol Cell 2019. |
Link to this post | posted 27 Dec, 2021 20:35 | |
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Ah, so you will have 2 different genes for the domains. Great! debbie |
Link to this post | posted 23 Dec, 2021 20:49 | |
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Chris, I added this, but I have a question. Are there 2 endolysin genes in this genome? Lysin genes are notorious for not having all domains match existing domains in the databases that we use. By that I mean, we can call a lysin A because ONE of the domains hit previously studied endolysins. so in the case of the gene you are interested in, is it possible that the 34% not covered is the missing protease domain? so the gene is a whole endolysin and not a gene broken into 2 pieces? I would recommend that we call the gene an endolysin if no protease domain is identified. Does that make sense? Would you also provide the genome/gene number to list it is an example int he function list. Thanks, debbie |
Link to this post | posted 17 Dec, 2021 17:45 | |
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Hi Ping, We have seen this before. I would call gene 2 "terminase, small subunit", gene 3 "terminase large subunit (ATPase domain)", and gene 4 "terminase large subunit (nuclease domain)". We have looked into this with the cluster AY phages and worked on a case study to show our investigation. It is still in draft form, but may be helpful. It is attached. |
Posted in: Cluster DT Annotation Tips → Terminase Genes
Link to this post | posted 13 Dec, 2021 18:06 | |
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Mary, Hi. Are you running as administrator? debbie |
Posted in: DNA Master → TbQueries