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All posts created by scaruso

| posted 14 Feb, 2018 13:28
scaruso avatar
scaruso
It is working now. I can see an update has been done, there may be causation in the correlation, though I do not know for sure.

Steve
Posted in: Web Phamerator → web phamerator phreezing up
| posted 23 Jan, 2018 16:24
scaruso avatar
scaruso
A new update seems to have it working again.

Steve
Posted in: DNA Master → %ANI
| posted 22 Jan, 2018 20:08
scaruso avatar
scaruso
Dan Russell
Steven Caruso
Those of us who use any of the alternate hosts still have to use the VM, sadly.

Steve

For now! I know the other Steve C. is working on having multiple databases available online, so at some point that will no longer be the case.

–Dan

Ever forward!

Steve
Posted in: SEA-PHAGES Virtual Machine → Student download of 2016 VM
| posted 22 Jan, 2018 20:02
scaruso avatar
scaruso
Those of us who use any of the alternate hosts still have to use the VM, sadly.

Steve
Posted in: SEA-PHAGES Virtual Machine → Student download of 2016 VM
| posted 18 Jan, 2018 16:05
scaruso avatar
scaruso
Lee,

I'm glad it isn't just me! I have been using OrthoAni here: https://www.ezbiocloud.net/tools and it's very nice, but you are limited to 10 genomes at a time, even if you install it.

Steve
Posted in: DNA Master → %ANI
| posted 17 Jan, 2018 18:36
scaruso avatar
scaruso
Here is what I see when I try to load genomes. Any help would be appreciated.

Steve
212Kb
Posted in: DNA Master → %ANI
| posted 13 Jan, 2018 16:47
scaruso avatar
scaruso
I do see the commands, but the GenBank files come up with no useful data according to DNAM. It's very odd. If I use one of my own files, it works great. But when I fetch by accession, I get empty files.

Any thoughts?

Steve
Edited 17 Jan, 2018 18:08
Posted in: DNA Master → %ANI
| posted 13 Jan, 2018 16:31
scaruso avatar
scaruso
Great, thank you!

Steve



Karen Klyczek
Hi Steve,

The new annotation guide has a section on genome comparisons. The direct link is https://seaphagesbioinformatics.helpdocsonline.com/article-89 (may require login in), or go to Mechanics > DNA Master > DNA Master Genome Comparison Tool in the left panel.

The guide suggests searching by accession number. But if the NCBI search is not working for some reason, you can also add genomes to the database by opening a .dnam file (or opening a fasta file and auto annotating) and using the Genome menu > Add to database. Then use Tools > Genome comparison > Manual to select genomes to analyze. Click on each genome and click the Add button, then click Analyze. ANIs are found in the Pairwise summaries tab. Note that the default is to show 16S identity, which will be zero for phage genomes. Select Average Nucleotide Identity from the pull-down menu.

(The map comparison tab is also super useful - you can create a map from a modified .dnam file and compare it to other phages.)

Karen
Posted in: DNA Master → %ANI
| posted 13 Jan, 2018 16:29
scaruso avatar
scaruso
Let me amend this a bit. I am able to run the test, still. But I am always getting "Unknown" now for my phage name. It only happens with files pulled from GenBank, though it doesn't matter if I add it directly to the Genome Manager, or open it and then add it. DNAM files I add that are my own retain their identifying information.

Steve
Posted in: DNA Master → %ANI
| posted 12 Jan, 2018 23:09
scaruso avatar
scaruso
Anyone,

OK, so I am stumped. I used to be able to do something in DNA Master that I can't seem to be able to do all of a sudden. Calculate the %ANI.

My only reference is the few lines in the addendum 'Exploring Bactriophage Biology, 2013,' so if anyone has a better guide, I would be grateful for it.

I have tried to add the phage genomes to the Genome Manager via NCBI search, bu what is showing up is "Unknown" in the Organism with the file name, Taffo16 complete genome, for example, under replicon. When I add more phages, I end up with more "Unknowns," each of which becomes visible separately as a single replicon. That isn't what I saw before. Then, when I run the Genome Comparison, I get no results. Nada.

Yet, it used to work. So I don't know what I forgot, or why it stopped working.

Any help would be gratefully accepted and lauded.

Steve
Posted in: DNA Master → %ANI