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All posts created by debbie

| posted 09 Dec, 2020 01:35
Kirk,
I'll weigh in. I like the way you are thinking, I would call this gene. Easily if it were in the middle somewhere; with trepidation that it is at the end of the genome. None of our commonly used programs 'like' genes that wrap around the end of the genome. GenBank consistently asks us if that is a really thing because we report a 'linear' genome with a gene that wraps around the ends. It is difficult to grasp that a phage genome circularizes, go figure! Phamerator is also not able to easily display a wrap around gene. If you look carefully at genome with an end-wrap around gene (like in some of the cluster C1 genomes), you will find what looks like a vertical random number displayed on a phamerator map at the midpoint of the genome. So while it is a great find, it is very unsatisfying to see it displayed. I want to link this to the cluster specific tips forums, because it may be the only place where this gene is celebrated.
As a footnote, when identifying base 1 of a circularly permuted genome I try very hard to find a gap, so i don't do this. Darn if the biology didn't catch me.
Curious what others might think about it all.
Thanks!
debbie
Posted in: Gene or not a Genegene at end of some EK1s?
| posted 04 Dec, 2020 12:45
Hi Kirk (and all),
The fix will be posted on Monday, December 7, 2020.
debbie
Posted in: DNA MasterGenome Comparison
| posted 03 Dec, 2020 04:05
Hi Kirk,
I can verify the same results that you obtained. I have sent an email to Jeffrey. I'll keep you posted.
debbie
Posted in: DNA MasterGenome Comparison
| posted 19 Nov, 2020 06:24
Hi WUSTL,
I have added "NAD-dependent deacetylase" to the list of approved functions! Thanks for identifying it!
debbie
Posted in: Request a new function on the SEA-PHAGES official listNAD-dependent deacetylase
| posted 17 Nov, 2020 11:34
Hi Amanda,
I think you are right. I will get that corrected.
Thanks,
debbie
Posted in: AnnotationPhage Jinkies - error in annotation?
| posted 11 Nov, 2020 20:57
Hi Christina and Nikki,
I think I would first rely on the coding potential and call the longer version of 71. While I would likely fill in this space with genes of the 4 bp overlap variety when I didn't have compelling coding potential choices, i like the coding potential better here.

While this may not help (but I haven't looked lately), there is a paper with mass spec for the genes of some of the Cluster J phages. I am sure if we had evidence of the 2 genes for the phages in that paper, we would have called them. From my quick glance, we did not.
https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0069273

debbie
Posted in: Choosing Start SitesLO or insert gene in J cluster Beem
| posted 07 Nov, 2020 18:50
To fix a "Key Violation" error, this should work:

Make yourself a backup directory on your desktop (name it something like
OldRecentFiles)
Then browse to C:/ProgramFiles/DNA Master/DMDB

There will be a bunch of files in there that all start with "RecentFile"

Move all of those into the new backup directory on your Desktop just in
case.

Then restart DNA Master. It will say that it can't find the RecentFile DB
files, and will download new copies of them (this should happen
automatically). If not, click the button marked "Download from FTP site" at
the upper right hand corner of the table that pops up. You can then discard the files that you moved out.
Posted in: DNA MasterKey Violation
| posted 22 Oct, 2020 01:06
Thanks Chris!
Posted in: Cluster A Annotation TipsVIP2-like toxin/ ADP-ribosyltransferase
| posted 21 Oct, 2020 19:12
Hi Parks,
I am not sure, but wanted to give you some more to think about or do.
See the attached picture and look at the sequence at 9731. A more canonical slippage, but really upstream of the stop of the "G" part of the G/T gene.

What would be helpful is to check out the other CZ1s and see if a consensus sequence is apparent in that place. Alignments are in order!

I do like the sequence, but I don't like how upstream it is…. need more info and to think about it.

debbie
Posted in: Frameshifts and IntronsCZ1 Tail assembly proteins
| posted 09 Oct, 2020 17:20
Sorry for the delay in this response.
I know of no fool-proof way to force induction. The literature describes UV and mitomycin C as agents. We have found that spotting one culture (or the supernatant of one) on a lawn of another will identify released phage of a prophage.
I think that is all i have for now.
debbie
Posted in: Lysogeny/ImmunityInducing phages from lysogeny to lytic cycle