SEA-PHAGES | %ANI

Link to this post \| posted 12 Jan, 2018 23:09
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

Link to this post | posted 12 Jan, 2018 23:09

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

Link to this post \| posted 13 Jan, 2018 16:23
kklyczek	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

Link to this post | posted 13 Jan, 2018 16:23

kklyczek

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

Link to this post \| posted 13 Jan, 2018 16:29
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

Link to this post \| posted 13 Jan, 2018 16:31
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

Link to this post | posted 13 Jan, 2018 16:31

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

Link to this post \| posted 13 Jan, 2018 16:47
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

Link to this post \| posted 17 Jan, 2018 18:36
scaruso	Here is what I see when I try to load genomes. Any help would be appreciated. Steve 212Kb

Link to this post \| posted 17 Jan, 2018 20:24
lhughes	Steve, I have always been successful in doing this in the past, and it gave me the same problem just now when I tried it. My DNA Master shows Build 2534 (14 Sep 2017). The only other thing that I know has changed on my computer is that I recently did an update to the most recent version of Windows 10. Help! I'm going to need to be able to download some more genomes soon for some QC I'm working on. Lee

Link to this post | posted 17 Jan, 2018 20:24

lhughes

Steve,

I have always been successful in doing this in the past, and it gave me the same problem just now when I tried it.

My DNA Master shows Build 2534 (14 Sep 2017).

The only other thing that I know has changed on my computer is that I recently did an update to the most recent version of Windows 10.

Help! I'm going to need to be able to download some more genomes soon for some QC I'm working on.

Lee

Link to this post \| posted 18 Jan, 2018 16:05
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

Link to this post \| posted 23 Jan, 2018 16:24
scaruso	A new update seems to have it working again. Steve

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