Link to this post | posted 13 Jan, 2022 17:15

debbie

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

Link to this post | posted 12 Jan, 2022 12:15
debbie	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

Link to this post | posted 05 Jan, 2022 21:06
debbie	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! Edited 21 Jun, 2022 17:39

Link to this post | posted 30 Dec, 2021 14:08

debbie

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. Edited 30 Dec, 2021 14:15

Link to this post | posted 27 Dec, 2021 20:35
debbie	Ah, so you will have 2 different genes for the domains. Great! debbie

Link to this post | posted 23 Dec, 2021 20:49

debbie

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 Edited 23 Dec, 2021 20:50

Link to this post | posted 17 Dec, 2021 17:45
debbie	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. 789Kb

Link to this post | posted 13 Dec, 2021 18:06
debbie	Mary, Hi. Are you running as administrator? debbie

Link to this post | posted 13 Dec, 2021 17:44
debbie	Hi all, Did you go back through this forum post and unpack and repack your DNA Master file? That is the typical way to fix this. https://seaphagesbioinformatics.helpdocsonline.com/article-104 It is tedious, so be patient. Let me know if that corrects the problem. If not, please send me the file. Thanks, debbie

Link to this post | posted 12 Dec, 2021 00:22
debbie	Maybe the different pham gene is actually in a different frame. What do you think? debbie