Link to this post | posted 21 Jan, 2022 18:06
debbie	Yes. That matches the page I attached above. But don't get confused. It is not what appears in the Glimmer and GeneMark fields that is important. They could actually be empty. What is important is that the check box is checked and the the unlock code is entered.

Link to this post | posted 20 Jan, 2022 21:51
debbie	Chris, We run Glimmer and Genemark on Pitt servers, so the update from 2017 is no longer applicable. debbie

Link to this post | posted 20 Jan, 2022 19:29
debbie	Chris, I am not sure what you are answering but do your DNA master preference panes look like this? Edited 20 Jan, 2022 19:40 637Kb

Link to this post | posted 19 Jan, 2022 01:22
debbie	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

Link to this post | posted 14 Jan, 2022 22:44

debbie

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

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