Link to this post | posted 30 Mar, 2023 17:52

debbie

Hi all, I just checked Wizard, and genes 16 (capsid maturation protease), 19 (major capsid hexamer protein) and 20 (Hypotheticall Protein) are all correct at phagesDB, Phamerator and in the Genbank file KU998234. They are disparate in the RefSeq file (NC_030913) at GenBank, BUT we have no control over their updates. Avoid RefSeq files as much as possible, because we cannot update them. Since Phamerator and phagesDB are informed by the same data set, they will always be the same unless you catch them in their updates. As for forums and such, since most folks ask questions when their genome is in draft form, lease ignore the number and refer to a gene by its stop. Currently as we are curate files (for functional calls) that information goes to GenBank first, then those changes are recognized and phamerated. that output is then picked up web Phamerator, phagesdb, starterator and their outputs are then posted. The timing for each program is automated and set differently for each one, but as updates post, the rest is then processed and posted pretty quickly. debbie

Link to this post | posted 30 Mar, 2023 16:18
debbie	Hi Beth, Before trying anything else, have your students close the program (maybe even restart their computer) and then try again. debbie

Link to this post | posted 29 Mar, 2023 12:54
debbie	I am willing to call this a head-to-tail stopper because the first hit is to gp20 of L5. while we have not updated the label of that gene, when you HHpred it, it is a good hit to the 5A21_G project, which is the gene that we are assigning the function had-to-tail stopper. debbie

Link to this post | posted 29 Mar, 2023 12:44
debbie	I would call this the helicase loader. I am not sure of the answer to your questions, but it is in the neighborhood. debbie

Link to this post | posted 24 Mar, 2023 21:28

debbie

Hi Adam, My answer is I don't know. This cluster of genomes is not like the others. It is a podo and I am not sure it fits the canonical features of podos. In order to answer this question, a review of podovirus structures is warranted. What are the canonical featured of them? So a deep dive into the literature is warranted here. Next, the cryoEM data is pouring in to the PDB, so what we have access to now vs when this cluster first appeared has grown. Next, in the literature you can find good reviews about podos and myos tails(and learn that the tail structures of siphos is a bit more elusive). We'll need to apply that to this. Next, your are cherry-picking one gene is a very non-canonical place in the genome. Structural genes frequently hit heads and tails and until we can clearly determine what we have going on here, I recommend that we prudently wait on jumping the gun. Finally, the same terminology doesn't always cross from sipho, myo and podo. So some thought will be required. Keep us posted as you do your investigations. debbie

Link to this post | posted 23 Mar, 2023 15:58
debbie	Veronique, I believe that this issue is outside of DNA Master's reach. Something it wanted to contact couldn't. (or something like that.) Regardless, I would restart my computer and then bet my nickel that it will disappear. debbie

Link to this post | posted 19 Mar, 2023 23:05
debbie	Using the phamerator numbers I would likely not call either 39 or 40. 34296 - 34397 has enough (though slight) coding potential for me to consider calling this one. No Other FF has this sequence. Note that this genome has 2 tRNAs, make sure there is not any overlap between genes/tRNAs.

Link to this post | posted 18 Mar, 2023 00:05
debbie	Excellent! Yay!

Link to this post | posted 17 Mar, 2023 23:59
debbie	Hi! I could call 41673-41810. There is a nib of coding potential and that if fits with 4bp overlaps at both ends is compelling. I think the coding potential is there for 41974-42225. However, I am not sure about the last one 42293-42394. I don't think that i would call it. debbie

Link to this post | posted 17 Mar, 2023 16:23
debbie	Amanda, This sounds like a connection is busted between the windows tools DNA Master uses and DNA Master. You have to get them back. The simplest way forward may be to totally uninstall and then reinstall it on your machine. If you haven't turned your machine off and then back on, that might be a first try. debbie