SEA-PHAGES | All posts created by DanRussell

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Link to this post \| posted 26 Jan, 2018 20:48
DanRussell	GregFrederick@letu.edu We are getting a lot of skipped genes of autoannotated genes. We can go in and blast them individually but most still fail. We can ad do use BlastP on phagesDB but then the documentation is not in the Blast section of DNA Master and it is difficult to confirm that students have actually done this analysis. I do not think I ever saw these skipped Blasts on previous genomes. But I have not done as many as many of you. Thoughts? Is it a server problem, something with our genome annotation or something else? Thanks. greg Hi Greg, To be clear: your problem is with BLAST, not auto annotation itself? Meaning you get all the features, but only some of them have BLAST results? BLASTing all genes can sometimes end up with genes being skipped, especially if done during peak hours. What phage are you working on? –Dan

Link to this post | posted 26 Jan, 2018 20:48

GregFrederick@letu.edu
We are getting a lot of skipped genes of autoannotated genes. We can go in and blast them individually but most still fail.

We can ad do use BlastP on phagesDB but then the documentation is not in the Blast section of DNA Master and it is difficult to confirm that students have actually done this analysis.

I do not think I ever saw these skipped Blasts on previous genomes. But I have not done as many as many of you.

Thoughts? Is it a server problem, something with our genome annotation or something else?

Thanks. greg

Hi Greg,

To be clear: your problem is with BLAST, not auto annotation itself? Meaning you get all the features, but only some of them have BLAST results?

BLASTing all genes can sometimes end up with genes being skipped, especially if done during peak hours. What phage are you working on?

–Dan

Posted in: DNA Master → Auto-annotation fix for fall 2017 and later

Link to this post \| posted 26 Jan, 2018 20:46
DanRussell	ptsourkas Still not working for me, as of January 24 2018. I get "Glimmer failure" and "Annotation failure". Thanks, Philippos Hi Philippos, Is your DNA Master up to date? If you run Update does all look good? Any other weird errors popping up? I think the servers are working. You've entered the proper access code in the linked document? –Dan

Posted in: DNA Master → Auto-annotation fix for fall 2017 and later

Link to this post \| posted 22 Jan, 2018 20:04
DanRussell	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

Posted in: SEA-PHAGES Virtual Machine → Student download of 2016 VM

Link to this post \| posted 22 Jan, 2018 19:59
DanRussell	Randall DeJong Dan Russell, I am having a real issue with getting 2017 SEA VM working on our Windows 10 computers. Can you get me the 2016 SEA VM that is 32 bit? Cal Keen ckeen@calvin.edu Hi Cal, Did you see my email response? In short: we're not recommending that you install the Virtual Machine at all this year, unless you have a specific need for it. Do you want to proceed with installing anyway? –Dan

Link to this post | posted 22 Jan, 2018 19:59

DanRussell

Randall DeJong
Dan Russell,
I am having a real issue with getting 2017 SEA VM working on our Windows 10 computers. Can you get me the 2016 SEA VM that is 32 bit?

Cal Keen
ckeen@calvin.edu

Hi Cal,

Did you see my email response? In short: we're not recommending that you install the Virtual Machine at all this year, unless you have a specific need for it. Do you want to proceed with installing anyway?

–Dan

Posted in: SEA-PHAGES Virtual Machine → Student download of 2016 VM

Link to this post \| posted 17 Jan, 2018 17:58
DanRussell	Hi Claire, I just added a "Last modified" date to the Google Sheet. It should auto-update anytime the list is changed and saved. The date itself is in cell B1. Hope that helps! –Dan

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

Link to this post \| posted 17 Jan, 2018 17:56
DanRussell	I think perhaps our servers were just down around Jan 12. Is it working now? –Dan

Posted in: DNA Master → Auto-annotation fix for fall 2017 and later

Link to this post \| posted 03 Jan, 2018 16:30
DanRussell	noverby Dan, Hope your holidays have been going well! Just checking in on the status of the 2018 VM? I'd like to work on getting our updated task sequence prepared and ready to install over our J-Term. If the download links are available, that would be much appreciated! Thank you for all that you do! Nate Hi Nate, There will be no new VM for this academic year. Partly because Phamerator and Starterator reports are now available on the web, we decided that the VM would be optional for schools this year. If they want to, they can use the 2017 VM, but most functions should be available via the web now. –Dan

Link to this post | posted 03 Jan, 2018 16:30

DanRussell

noverby
Dan,

Hope your holidays have been going well!

Just checking in on the status of the 2018 VM? I'd like to work on getting our updated task sequence prepared and ready to install over our J-Term. If the download links are available, that would be much appreciated!

Thank you for all that you do!

Nate

Hi Nate,

There will be no new VM for this academic year. Partly because Phamerator and Starterator reports are now available on the web, we decided that the VM would be optional for schools this year. If they want to, they can use the 2017 VM, but most functions should be available via the web now.

–Dan

Posted in: SEA-PHAGES Virtual Machine → Student download of 2016 VM

Link to this post \| posted 18 Dec, 2017 16:35
DanRussell	Hi Sarah, From BLASTing Phergie on PhagesDB, it looks like the break is caused by the insertion of a single C. In those other closely-related genomes, there are 4 Cs, but in Phergie there are 5. I went and found the assembly for Phergie, and in that region you can see that there are plenty of high-quality reads that all have 5 Cs isntead of 4. So it's not a sequencing error! Looks like a real mutation that broke that gene into two. –Dan

Link to this post | posted 18 Dec, 2017 16:35

DanRussell

Hi Sarah,

From BLASTing Phergie on PhagesDB, it looks like the break is caused by the insertion of a single C. In those other closely-related genomes, there are 4 Cs, but in Phergie there are 5.

I went and found the assembly for Phergie, and in that region you can see that there are plenty of high-quality reads that all have 5 Cs isntead of 4.

So it's not a sequencing error! Looks like a real mutation that broke that gene into two.

–Dan

Posted in: Gene or not a Gene → Lysin A split in 2 or sequencing error-B1 cluster

Link to this post \| posted 11 Dec, 2017 13:25
DanRussell	mdgainey Thanks for posting this Nick. Dan, I have one podo with an unstable capsid and would like to try to seq/assemble with just an RNase treatment. Dan do you have any basic tips to reduce host DNA contamination in my prep to hopefully achieve a successful assembly without DNase treatment, sounds like it might be fine but if I could stack the deck a bit that would be great. This one grows really well so high titer should not be a problem. Maria Hey Maria, I don't really have any good tips to reduce the host DNA, but my sense is I'd try sequencing it and see what comes out. If the host DNA really is overwhelming, then it's back to the drawing board, but I think there's a decent chance the phage sequence would stand out from the bacterial chunks, and then you'd be done. So I'd just try prepping and sequencing without DNAse and see what comes out, then only worry about reducing the host DNA if that first attempt didn't work. –Dan

Link to this post | posted 11 Dec, 2017 13:25

DanRussell

mdgainey
Thanks for posting this Nick. Dan, I have one podo with an unstable capsid and would like to try to seq/assemble with just an RNase treatment. Dan do you have any basic tips to reduce host DNA contamination in my prep to hopefully achieve a successful assembly without DNase treatment, sounds like it might be fine but if I could stack the deck a bit that would be great. This one grows really well so high titer should not be a problem.
Maria

Hey Maria,

I don't really have any good tips to reduce the host DNA, but my sense is I'd try sequencing it and see what comes out. If the host DNA really is overwhelming, then it's back to the drawing board, but I think there's a decent chance the phage sequence would stand out from the bacterial chunks, and then you'd be done. So I'd just try prepping and sequencing without DNAse and see what comes out, then only worry about reducing the host DNA if that first attempt didn't work.

–Dan

Posted in: Phage Discovery/Isolation → Yield and degradation of DNA isolated by new protocol

Link to this post \| posted 04 Dec, 2017 16:22
DanRussell	In 2017, NCBI decided to no longer host public instances of GeneMark and Glimmer, which were used by DNA Master to perform auto-annotations. If your copy of DNA Master is failing to auto-annotate, see the post below about how to get it working again. https://seaphages.org/blog/2017/10/27/auto-annotation-fix-dna-master/ –Dan

Posted in: DNA Master → Auto-annotation fix for fall 2017 and later

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