SEA-PHAGES | DNAM failing to use proper translation code

Link to this post \| posted 26 Mar, 2019 15:24
jross1025	Dear All: Last year I noticed almost accidentally that I had seemingly autoannotated a genome using the so-called "standard" code. Not sure when this first actually popped up because seeing "standard" anything isn't necessarily going to set off red flags, but I'm almost positive that at the time my preferences specified "bacterial and plant plastid" code, which is the correct one. So this most recent year, it crops up again. I do uninstall/reinstall, re-set the preferences, again "bacterial and plant plastid" is selected, and again DNAM is autoannotating using (so it claims….) the "standard" code. Just yesterday evening I observed the same thing happening in one of our computer lab machines, so this is not specific either to my computer or to my download (lab computer software is added by an IT person, who pulls down his own copies of the program from the web). Also just yesterday for the first time I saw a quite different code pop up "CmB….something…." which I think is not even in the drop down window menu. I saw this both in the lab and my own machine, so again whatever this is transcends particular hardware/download copy. I'm not sure it's doing any harm–Ugenie5, and maybe LilDestine–were both autoannotated on–again supposedly–"standard" code, and both are in Genbank without having been sent back to me, but this is troubling nonetheless. Any thoughts? Edited 26 Mar, 2019 15:25

Link to this post | posted 26 Mar, 2019 15:24

Dear All: Last year I noticed almost accidentally that I had seemingly autoannotated a genome using the so-called "standard" code. Not sure when this first actually popped up because seeing "standard" anything isn't necessarily going to set off red flags, but I'm almost positive that at the time my preferences specified "bacterial and plant plastid" code, which is the correct one. So this most recent year, it crops up again. I do uninstall/reinstall, re-set the preferences, again "bacterial and plant plastid" is selected, and again DNAM is autoannotating using (so it claims….) the "standard" code. Just yesterday evening I observed the same thing happening in one of our computer lab machines, so this is not specific either to my computer or to my download (lab computer software is added by an IT person, who pulls down his own copies of the program from the web). Also just yesterday for the first time I saw a quite different code pop up "CmB….something…." which I think is not even in the drop down window menu. I saw this both in the lab and my own machine, so again whatever this is transcends particular hardware/download copy. I'm not sure it's doing any harm–Ugenie5, and maybe LilDestine–were both autoannotated on–again supposedly–"standard" code, and both are in Genbank without having been sent back to me, but this is troubling nonetheless. Any thoughts?

Edited 26 Mar, 2019 15:25

Link to this post \| posted 26 Mar, 2019 19:00
debbie	Joe, I think you are confusing apples and oranges here. The 'standard code" settings have no effect anywhere in auto-annotation. Also if you have chosen ATG, GTG, and TTG start codons in the Translation tab of the Local Settings in your preferences, DNA Master will display them. You can select "Bacteria and Plant Plastid Code" in the New Features Tab of the Local Settings. Is that what changes? What is changing on you? debbie

Link to this post | posted 26 Mar, 2019 19:00

debbie

Joe,
I think you are confusing apples and oranges here. The 'standard code" settings have no effect anywhere in auto-annotation. Also if you have chosen ATG, GTG, and TTG start codons in the Translation tab of the Local Settings in your preferences, DNA Master will display them.

You can select "Bacteria and Plant Plastid Code" in the New Features Tab of the Local Settings. Is that what changes?

What is changing on you?
debbie

Link to this post \| posted 26 Mar, 2019 19:48
jross1025	Debbie Jacobs-Sera Joe, I think you are confusing apples and oranges here. The 'standard code" settings have no effect anywhere in auto-annotation. Also if you have chosen ATG, GTG, and TTG start codons in the Translation tab of the Local Settings in your preferences, DNA Master will display them. You can select "Bacteria and Plant Plastid Code" in the New Features Tab of the Local Settings. Is that what changes? What is changing on you? debbie Deb: If you go into an autoannotation, Features tab, Description sub-tab, there's a dropdown window called "translation table"–that's what I'm referring to. "Bacteria and Plant Plastid code" is what is chosen in preferences under "new features" but it's displaying "standard code" when you actually run the autoannotation. I'm really just trying to determine if this is going to cause problems later on. I suspect it isn't, but it's worrying….

Link to this post | posted 26 Mar, 2019 19:48

jross1025

Debbie Jacobs-Sera
Joe,
I think you are confusing apples and oranges here. The 'standard code" settings have no effect anywhere in auto-annotation. Also if you have chosen ATG, GTG, and TTG start codons in the Translation tab of the Local Settings in your preferences, DNA Master will display them.

You can select "Bacteria and Plant Plastid Code" in the New Features Tab of the Local Settings. Is that what changes?

What is changing on you?
debbie

Deb:
If you go into an autoannotation, Features tab, Description sub-tab, there's a dropdown window called "translation table"–that's what I'm referring to. "Bacteria and Plant Plastid code" is what is chosen in preferences under "new features" but it's displaying "standard code" when you actually run the autoannotation. I'm really just trying to determine if this is going to cause problems later on. I suspect it isn't, but it's worrying….

Link to this post \| posted 27 Mar, 2019 13:03
welkin	Hi Joe– No, it won't cause any problems. As long as those alternate start codons are selected in the preferences you don't need to worry about the standard vs bacteria codes here. We reset the entire annotation to the bacterial code enmass when we submit to GenBank.

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DNAM failing to use proper translation code