SEA-PHAGES | All posts created by DanRussell

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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

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

Link to this post \| posted 09 Nov, 2017 20:54
DanRussell	I think for small stuff like that you can just email Welkin, since she's the keeper of the list at the moment. That's probably simplest. If it's a larger issue that others might be wondering about, then just post on the forum itself. Welkin recently posted a "READ THIS FIRST" post with some instructions. https://seaphages.org/forums/topic/4440/ –Dan

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

Link to this post \| posted 31 Oct, 2017 15:31
DanRussell	Hi Chris, Without any other super-obvious place to put it, I added it as a blog entry. It's brand-new (Steve found it moments after putting it up) so we haven't had a chance to cross-link everything (guides, other pages) to it yet, but we will soon! https://seaphages.org/blog/2017/10/30/official-function-list/ –Dan

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

Link to this post \| posted 30 Oct, 2017 19:57
DanRussell	Steven Caruso 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 Thanks for the eagle eyes, Steve. I'll let Welkin (the master curator) know. –Dan

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

Link to this post \| posted 24 Oct, 2017 15:40
DanRussell	Hi Katie, I think this error is due to not having a certain library installed on the particular version of Windows that's running. That library wasn't required until after the update earlier this year to use secure NCBI servers. I think I came across that error myself, and in my notes I have that I went to the link below and installed the Visual C++ package there, then restarted and it worked. ~~https://www.microsoft.com/en-us/download/details.aspx?id=5555~~ UPDATE Sep 2021: The link above no longer works, but the file can be found at the link below now. Download it from within Windows and then run it, and make sure you close DNA Master and restart Windows before trying to BLAST again. https://phagesdb.org/static/vcredist_x86.exe Hopefully that helps, –Dan Edited 03 Sep, 2021 15:03

Link to this post | posted 24 Oct, 2017 15:40

DanRussell

Hi Katie,

I think this error is due to not having a certain library installed on the particular version of Windows that's running. That library wasn't required until after the update earlier this year to use secure NCBI servers. I think I came across that error myself, and in my notes I have that I went to the link below and installed the Visual C++ package there, then restarted and it worked.

~~https://www.microsoft.com/en-us/download/details.aspx?id=5555~~

UPDATE Sep 2021: The link above no longer works, but the file can be found at the link below now. Download it from within Windows and then run it, and make sure you close DNA Master and restart Windows before trying to BLAST again.

https://phagesdb.org/static/vcredist_x86.exe

Hopefully that helps,
–Dan

Edited 03 Sep, 2021 15:03

Posted in: DNA Master → SSL error

Link to this post \| posted 19 Oct, 2017 16:05
DanRussell	Hi Heather, As long as everything is precisely typed into Phamerator, I think this is likely to be a Phamerator-Ubuntu issue rather than a PhamDB issue. Check out the suggestions in this post and see if any of those might help. Sometimes, weird stuff can happen on the VM which sends Phamerator into strange cycles, but Steve had a couple suggestions. https://seaphages.org/forums/topic/246/?page=1#post-1338 –Dan

Link to this post | posted 19 Oct, 2017 16:05

DanRussell

Hi Heather,

As long as everything is precisely typed into Phamerator, I think this is likely to be a Phamerator-Ubuntu issue rather than a PhamDB issue. Check out the suggestions in this post and see if any of those might help. Sometimes, weird stuff can happen on the VM which sends Phamerator into strange cycles, but Steve had a couple suggestions.

https://seaphages.org/forums/topic/246/?page=1#post-1338

–Dan

Posted in: Phamerator → PhamDB: Make your own Phamerator databases

Link to this post \| posted 29 Sep, 2017 14:16
DanRussell	grosej Hi Dan, I am wondering if there is a way to merge two PhamDB databases, such as by merging the mysql files? thanks! Julianne Grose Hi Juli, I don't know if you can merge two databases easily with PhamDB, but PhamDB definitely makes it easy to add phages that are in the system to other databases in the system without having to re-enter them. You can use the "Add to Database" function. –Dan

Link to this post | posted 29 Sep, 2017 14:16

DanRussell

grosej
Hi Dan,
I am wondering if there is a way to merge two PhamDB databases, such as by merging the mysql files?
thanks!
Julianne Grose

Hi Juli,

I don't know if you can merge two databases easily with PhamDB, but PhamDB definitely makes it easy to add phages that are in the system to other databases in the system without having to re-enter them. You can use the "Add to Database" function.

–Dan

Posted in: Phamerator → Phams

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