SEA-PHAGES | All posts created by scaruso

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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

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

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

Posted in: DNA Master → %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

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

Link to this post \| posted 30 Oct, 2017 19:55
scaruso	The approved list you just posted includes: 139 Toxin in toxin/antitoxin system, HicB-like Xeno_32 In addition to listing HicB-like as the anti-toxin. I believe HicA is the toxin and HicB is the anti-toxin and that HicB should not be listed as both the toxin and anti-toxin. Steve

Posted in: Request a new function on the SEA-PHAGES official list → Approved list

Link to this post \| posted 21 Jul, 2017 17:03
scaruso	The direct: http://cobamide2.bio.pitt.edu/computer.htm is now working.

Posted in: DNA Master → DNA Master Issue

Link to this post \| posted 21 Jul, 2017 15:44
scaruso	So better NKF? A shame. This is an interesting looking hit. It's compelling, and makes sense. And in fact, restriction enzymes and Ocr do have something in common, of course, right? Binding (or mimicking) DNA. Thanks for your help! Steve Edited 21 Jul, 2017 16:00

Posted in: Functional Annotation → Gene with homology to T7 Ocr gene

Link to this post \| posted 21 Jul, 2017 13:49
scaruso	I have a student that is unable to run DNAM on a home computer running W10, I assumed because he wasn't running running it as an Admin. He has since uninstalled to try and re-install, and can't because now the links are down. Both the direct and to the hosting web site. An update, crash, or something else? Steve

Posted in: DNA Master → DNA Master Issue

Link to this post \| posted 19 Jul, 2017 23:56
scaruso	Welkin, Great, thanks for taking a look. It looks interesting. MTKKLELAQYDYIEVLEDEIDVLERFNEYNGSTCVCDAITEIADAAVSIYPADLWKNAYEMKEYIEAAMSSGLCETPSGQQPDLDKI SAAGYYEYYSQLLYNNESEMYYNYIANIVNKWIETLNYEQLEKLDIDELDACIEHEKGDIDSNSYMEELEDIAKRIIAGFKVKVNKN DVWENHGDVDALDQGGIFIRPDEEQRHCYYVVKVDNLEYVTKEDKIRITDMYVDISDDWFDWAGIEAYSGTEESDDDIEKVLAVIDY HGAENFNPDIEDFEDKADAIEYLANMGIAIEEV I think you can still access HHPred links with the new system. Here are the hits: https://toolkit.tuebingen.mpg.de/#/jobs/Anthony_gp275 It doesn't extend throughout the entire length of the protein, but it is from a very different phage and is rather compelling. So, I am on the fence. As you can see. So, I suppose the way to look for a connection here is to see if the conserved residues being picked up by HHPred are the important G, A, L, and R? Steve Edited 20 Jul, 2017 13:27

Link to this post | posted 19 Jul, 2017 23:56

scaruso

Welkin,

Great, thanks for taking a look. It looks interesting.

MTKKLELAQYDYIEVLEDEIDVLERFNEYNGSTCVCDAITEIADAAVSIYPADLWKNAYEMKEYIEAAMSSGLCETPSGQQPDLDKI
SAAGYYEYYSQLLYNNESEMYYNYIANIVNKWIETLNYEQLEKLDIDELDACIEHEKGDIDSNSYMEELEDIAKRIIAGFKVKVNKN
DVWENHGDVDALDQGGIFIRPDEEQRHCYYVVKVDNLEYVTKEDKIRITDMYVDISDDWFDWAGIEAYSGTEESDDDIEKVLAVIDY
HGAENFNPDIEDFEDKADAIEYLANMGIAIEEV

I think you can still access HHPred links with the new system. Here are the hits:

https://toolkit.tuebingen.mpg.de/#/jobs/Anthony_gp275

It doesn't extend throughout the entire length of the protein, but it is from a very different phage and is rather compelling. So, I am on the fence. As you can see.

So, I suppose the way to look for a connection here is to see if the conserved residues being picked up by HHPred are the important G, A, L, and R?

Steve

Edited 20 Jul, 2017 13:27

Posted in: Functional Annotation → Gene with homology to T7 Ocr gene

Link to this post \| posted 17 Jul, 2017 15:52
scaruso	I have a gene for which the top three HHPred hits are all >99% prob, Eval 10^-21, ident 22% to the phage T7 Ocr gene (gene 0.3), which protects DNA from attack by the host's type I restriction enzymes. So, I am wondering what to call this. In reverse order of specificity: Ocr Ocr-like protein DNA bending protein DNA binding protein Thoughts and suggestions? Steve Edited 17 Jul, 2017 15:53

Posted in: Functional Annotation → Gene with homology to T7 Ocr gene

Link to this post \| posted 11 Jul, 2017 17:08
scaruso	They are supposed to be more stable, though I haven't tested it myself.

Posted in: Streptomyces → How to prepare spore suspension?

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