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All posts created by welkin

| posted 26 Feb, 2020 19:07
ANI in DNA MAster is calculated between pairs of genes that share protein sequence similarity at a preset threshold. Not all ANI calculators do this, some are simply whole genome without regard to gene content.
So yes, span length matters, for ANI in DNA MAster.
Posted in: Phage BiologyANI interpretation w/ span-length coverage
| posted 21 Feb, 2020 18:32
I looked carefully at gene one of these too– and although it aligned to the large subunit, the alignment occurs in the middle of the functional domains, possibly interrupting them. SO we will call that gene hypothetical protein for now.
Posted in: Cluster AS Annotation TipsTerminase, large subunit
| posted 21 Feb, 2020 18:30
Upon even more examination—AS genomes appear to have a gene 1 with some alignment to the large subunit, but it is unclear if the domains are intact. So we are going to revert it to hypothetical protein. (10-21-19, 2-21-2020)
Posted in: Cluster AS Annotation Tipstwo small terminase subunits
| posted 13 Feb, 2020 15:14
Some of the students in my class that use Macs are having issues installing DNA Master. Is there any known compatibility issue with Catalina? It seems like the ones that are not having any issues are the ones who didn't upgrade to Catalina. Please let me know.
Hi German, if you mean running WINE on Catalina, yes there is an issue. See:

But if you are running virtual box and a Windows 10 VM, there is no problem.
Posted in: DNA MasterAuto-annotation fix for fall 2017 and later
| posted 04 Feb, 2020 18:11
Hi Jordan–
I am always interested in these teeny phages and how they are managing to do all the biology of the big ones.
In this case, I am not able to find an obvious integrase or par system or other mechanism by which lysogeny could be maintained. So I think your plan above is the right way to go— it is possible there is some sort of other unknown equivalent system here, but without bench work, it is hard to say. The integrase could also have been lost during purification– without more phages to compare to, who knows? HTHs all around!
Posted in: Singleton Annotation TipsBluefeather (singleton) lysogeny genes
| posted 03 Feb, 2020 12:56
Hi Jordan
I'll take a look!
Posted in: Singleton Annotation TipsBluefeather (singleton) lysogeny genes
| posted 14 Jan, 2020 17:55
I wish I knew!
I have yet to come across a protocol for a one-step growth curve in Actinobacteriophages that is accurate and repeatable.
in general, it takes about three hours to get from infection to burst, but the adsorption does not seem as synchronous as it should be, and so rather than a clear latent/burst curve, I see somewhat tiered bursts over many hours.
I would be interested to see your protocol that is supposed to work.
Posted in: Phage BiologyOne Step Growth Curve
| posted 08 Jan, 2020 18:22
Thanks for posting—
I agree– not enough information to include it as a function for now, but definitely worth pointing out and keeping an eye on.
Posted in: Functional AnnotationCluster DW - Beta protein?
| posted 06 Jan, 2020 19:42
Cluster GD phages have what appears to be two intact copies of the large subunit of the terminase, plus two more genes that encode large subunit of the terminase domains.
Posted in: Cluster GD Annotation Tipsmultiple terminases
| posted 23 Oct, 2019 18:25
Hi Amanda,
Debbie and I reviewed the evidence for the small terminase in the right arm of the genome and we don't think it holds up. We will be changing this function call to DNA binding protein or transcription factor, depending on the protein.
Posted in: Cluster AS Annotation TipsTerminase, large subunit