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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 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 15 Oct, 2019 15:42
while not the usual case, there are a few genes through the Actinobacteriophages that are oriented as you describe. So if it is conserved throughout the cluster, go ahead and call it.
Posted in: Annotationspace for a promoter when changing direction?
| posted 04 Oct, 2019 13:38
Hi Amy,
The only real way to tell if you have an intron is at the bench, so for the most part we do not add them to annotations.
The exception being cluster J, as you noted above, where we have bench data for one in the capsid gene of LittleE and one in a minor tail gene in BAKA. So if your phages is identical in sequence to one of the two that we've demonstrated are present at the bench, you should add them.

The comment about using Phamerator to find them only really works if an essential gene is split into two pieces in one phage where it is only present in one piece in the close relatives. This is how we discovered that LittleE and BAKA had introns in the first place— we knew that the capsid gene should only be one gene. So to use Phamerator, you'd need to know that genes are essential and should be only one piece— which doesn't apply to most of the phage genes as we do not know what most of them do.
If you have an intron identical to one of the previously characterized ones, you can use the nucleotide sequences in Phamerator to show you exactly where the boundaries are— just get the nucleotide sequence of each gene in question and then align them against each other using BLAST.
Posted in: Frameshifts and IntronsFinding introns
| posted 11 Sep, 2019 18:13
Hi Christine,
Do you mean changing transcription direction? Or just existing in different reading frames? The most common arrangement of genes that we see in phage genomes is a 4bp overlap, which leads to adjacent genes in different translational frames. So yes, that is quite common.
Posted in: Gene or not a GeneMultiple ORFs in GeneMark