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All posts created by afreise

| posted 24 Jan, 2024 01:00
thanks, Debbie! and thanks for the note about the preceding gene too!
Posted in: Singleton Annotation Tipstail assembly chaperones
| posted 23 Jan, 2024 23:50
We are having a tricky time with the putative tail assembly chaperone for Singleton RomansRevenge. Its closest relatives are cluster AP phages. Most AP phages do not annotate a TAC, but several do (e.g, PureGlobe5). Please see the attached PPT for data collection.

There is coding potential in the top reading frame on genemark for a potential new gene (RR_27), and the stop site looks like it would be 19980.

Though the first putative TAC gene in RomansRevenge (gp26) is in the same pham as PureGlobe5's first TAC gene, there are significant sequence differences.
I aligned them and looked for the slippery sequence in the same region I saw the shift in PureGlobe5, but I am not seeing any of the canonical slippery sequences in RomansRevenge_26.
Posted in: Singleton Annotation Tipstail assembly chaperones
| posted 22 Jan, 2024 17:38
The approved function list still lists the old evidence requirements (TmHmm, TOPCONS) for membrane proteins - could this be updated?
Posted in: AnnotationMembrane proteins
| posted 26 Dec, 2023 21:00
Good news! VMWare Fusion version 13.5 contains a built-in approach to installing WIndows 11 ARM version. All you have to do is install VMWare and then when the wizard pops up, select 'Get Windows from Microsoft". It will auto-download the ARM version. I used it and then downloaded DNA Master using Kristen's update package successfully.
Note: when you first boot Windows, you must click within the window and press a key within 5 seconds or it will time out. (more info:
Posted in: DNA MasterDNA Master on M1 Mac
| posted 03 Jun, 2023 15:32
Hi Dan - could we get a new forum for Cluster FP phages?
Posted in: Cluster-Specific Annotation TipsUsing This Forum
| posted 17 Mar, 2023 20:10
Ah! I should have tried the old off-and-on trick first (did it with DNA Master, but not the entire machine). That solved the problem. Thank you Debbie!
Posted in: DNA MasterDNA master parse error (and others)
| posted 16 Mar, 2023 23:51

I'm encountering some unexpected errors in DNA master. This is true for both old DNAM files I have previously successfully worked with, and a new one I made from the FASTA sequence.

When I open the file, I get an error that says: "Field 'Path' must have a value."

I'm able to work in the file from there, but when I add my notes to the documentation and parse, the feature table is coming up empty. Again, this is true using both new notes files and old ones that previously did work.

Other times I try to open a file and get "Stream write error". In this case the file does not open at all. But if I try again, it does sometimes open the file.

I have updated DNA Master and the problems persist. Any ideas on how to solve this?
Posted in: DNA MasterDNA master parse error (and others)
| posted 09 Feb, 2023 23:07
Hi Debbie et al.,

In the January 2023 faculty meeting you updated guidance on TMD prediction. As of now we are using just DeepTMHMM and looking for at least one TMD, about ~17-22aa long.

My question is…how close does that "~" need to be? If DeepTMHMM predicts a TMD of 15 or 16aa, are those close enough? Or does it need to fall WITHIN 17-22aa long?

Posted in: AnnotationMembrane proteins
| posted 08 Feb, 2023 16:28
Thank you Debbie!
Posted in: Cluster B Annotation TipsTail assembly chaperones?
| posted 08 Feb, 2023 01:52
Does anyone have any thoughts about this potential TAC gene in B1 phages? I'm going to submit my annotation soon and would love to finalize this gene before they get to SMART. Please see my attachment in the above post for all the info.

Posted in: Cluster B Annotation TipsTail assembly chaperones?