SEA-PHAGES | All posts created by DanRussell

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Link to this post \| posted 03 Mar, 2016 16:05
DanRussell	saleadon Hi Everyone, In "Exploring Bacteriophage Biology", one suggested bioinformatics experiment is to design cluster-specific DNA primers. The article mentions that there is a list of existing primers on phagesdb.org under “Phorum”. However, I can't find that. Has it been moved or deleted? Thanks, Steve Hi Steve, That document needs to be updated! Yes, the PhagesDB Phorum has indeed been deleted. And I'm not sure that we'd necessarily recommend that particular experiment either, since it has proved of limited use. It might be an interesting teaching/thought experiment…like: can you locate regions that are conserved in all the members of a subcluster? A cluster? Or not? (i.e., Is it even possible to design cluster-specific primers?) In any event, I know that Alex Peister at Morehouse College has been the de facto go-to person for cluster primers, so she would be a good resource if you're interested in the current state of those attempts. –Dan

Link to this post | posted 03 Mar, 2016 16:05

saleadon
Hi Everyone,
In "Exploring Bacteriophage Biology", one suggested bioinformatics experiment is to design cluster-specific DNA primers. The article mentions that there is a list of existing primers on phagesdb.org under “Phorum”. However, I can't find that. Has it been moved or deleted?
Thanks,
Steve

Hi Steve,

That document needs to be updated! Yes, the PhagesDB Phorum has indeed been deleted. And I'm not sure that we'd necessarily recommend that particular experiment either, since it has proved of limited use. It might be an interesting teaching/thought experiment…like: can you locate regions that are conserved in all the members of a subcluster? A cluster? Or not? (i.e., Is it even possible to design cluster-specific primers?)

In any event, I know that Alex Peister at Morehouse College has been the de facto go-to person for cluster primers, so she would be a good resource if you're interested in the current state of those attempts.

–Dan

Posted in: Phage Biology → PCR Primers

Link to this post \| posted 02 Mar, 2016 21:49
DanRussell	Hi Denise, Sounds like that would be enough for me to take a look! Let me know when they're posted and I'll see what I can see. –Dan

Posted in: Annotation → Locating Terminase Gene

Link to this post \| posted 29 Feb, 2016 19:48
DanRussell	Debbie Jacobs-Sera Hi all! I was just able to blast a gene (and repeated by Dan) in DNA Master. The Integer Overflow error is gone and my posted wait time was 31 seconds, with the blast data returned in about 1 1/2 minutes. I just started to Blast an entire genome and will keep you posted as to how that goes! We are back in business! Hopefully this is fixed, everyone! Nice job by Debbie bugging NCBI into cooperation. Let us know if you continue to have problems. You shouldn't need to update anything to have success, just try again. –Dan

Link to this post | posted 29 Feb, 2016 19:48

DanRussell

Debbie Jacobs-Sera
Hi all! I was just able to blast a gene (and repeated by Dan) in DNA Master. The Integer Overflow error is gone and my posted wait time was 31 seconds, with the blast data returned in about 1 1/2 minutes. I just started to Blast an entire genome and will keep you posted as to how that goes! We are back in business!

Hopefully this is fixed, everyone! Nice job by Debbie bugging NCBI into cooperation.

Let us know if you continue to have problems. You shouldn't need to update anything to have success, just try again.
–Dan

Posted in: DNA Master → BLAST in DNAM

Link to this post \| posted 25 Feb, 2016 18:34
DanRussell	Hi Denise, First of all, are you sure this is a circularly permuted genome? It's always possible that the phage already has ends of its own, then you don't have to worry about choosing them yourself. I can check that if you give me the sequence file and the sequencing reads. (Posting on Dropbox or Google Drive is a good way to move those large files.) If it truly is circularly permuted, I'm sure Debbie would be happy to take a look at potential Base 1 options. She's done this a lot! –Dan

Link to this post | posted 25 Feb, 2016 18:34

DanRussell

Hi Denise,

First of all, are you sure this is a circularly permuted genome? It's always possible that the phage already has ends of its own, then you don't have to worry about choosing them yourself. I can check that if you give me the sequence file and the sequencing reads. (Posting on Dropbox or Google Drive is a good way to move those large files.)

If it truly is circularly permuted, I'm sure Debbie would be happy to take a look at potential Base 1 options. She's done this a lot!

–Dan

Posted in: Annotation → Locating Terminase Gene

Link to this post \| posted 25 Feb, 2016 16:03
DanRussell	Hi Denise, Does this happen to be Beth or C3PO? –Dan

Posted in: Annotation → Locating Terminase Gene

Link to this post \| posted 25 Feb, 2016 15:25
DanRussell	Sebastian Schmeier Please the link as well Dan. Are there different links for Mac vs Win versions? I would need both. Can you please also sent me the student and faculty user/passwd please. Thank you very much, Sebastian ~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~ Sebastian Schmeier Lecturer in Bioinformatics/Genomics Institute of Natural and Mathematical Sciences Massey University Auckland, New Zealand +64 9 213 6538 :: +64 9 414 0800 ext 43538 s.schmeier@massey.ac.nz :: http://sschmeier.com ~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~ Just sent them. –Dan

Link to this post | posted 25 Feb, 2016 15:25

DanRussell

Sebastian Schmeier
Please the link as well Dan. Are there different links for Mac vs Win versions? I would need both.

Can you please also sent me the student and faculty user/passwd please.

Thank you very much,

Sebastian

~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~
Sebastian Schmeier
Lecturer in Bioinformatics/Genomics
Institute of Natural and Mathematical Sciences
Massey University Auckland, New Zealand
+64 9 213 6538 :: +64 9 414 0800 ext 43538
s.schmeier@massey.ac.nz :: http://sschmeier.com
~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~

Just sent them.

–Dan

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

Link to this post \| posted 24 Feb, 2016 20:35
DanRussell	Jeffrey Lawrence is aware of the issue and is working on it now. If he comes up with a fix and/or if there's anything to report, we'll let you know as soon as we do! –Dan

Posted in: DNA Master → BLAST in DNAM

Link to this post \| posted 24 Feb, 2016 14:49
DanRussell	Hi Keith et al, Yes, I'm seeing some slower peformance for sure in the VM DNA Master. For some functions, it's quite quick, but for others it drags. I hit a snag when I tried to import a fasta file that was about 170 kb long. It froze, and never made it through. I tried repeating, adjusting VM memory, etc., but nothing seemed to help. That would obviously be a dealbreaker, but perhaps we can figure out some workarounds or improvements. The 2017 SEA VM will use the newer version of Ubuntu, so perhaps those upgrades will help. I'm curious as to whether some of the problems might relate to the artificial PC file system that's set up by wine, and whether we can change some settings to improve along those lines. –Dan

Link to this post | posted 24 Feb, 2016 14:49

DanRussell

Hi Keith et al,

Yes, I'm seeing some slower peformance for sure in the VM DNA Master. For some functions, it's quite quick, but for others it drags. I hit a snag when I tried to import a fasta file that was about 170 kb long. It froze, and never made it through. I tried repeating, adjusting VM memory, etc., but nothing seemed to help. That would obviously be a dealbreaker, but perhaps we can figure out some workarounds or improvements. The 2017 SEA VM will use the newer version of Ubuntu, so perhaps those upgrades will help.

I'm curious as to whether some of the problems might relate to the artificial PC file system that's set up by wine, and whether we can change some settings to improve along those lines.

–Dan

Posted in: DNA Master → Beta Test: DNA Master within the SEA VM

Link to this post \| posted 24 Feb, 2016 14:45
DanRussell	Joseph Ross What do the X's mean? You have to mentally scoot the top line over a few spaces to line it up properly, but even still it's interesting that it recognizes some of the Xs as an identity to the target and some not. I've never seen this before. This is from LilDestine, in the product from the ORF that DNA Master calls starting at bp9002. It's a tail protein according to BLASTp at least. Hi Joe, Those Xs represent a "region of low complexity". What that basically means is that the amino acids there are quite similar to one another, or there are repetitive patterns, and as such they're bait for lots of meaningless alignments. Here's a link to NCBI's explanation. It's not something you should worry about, though! –Dan

Link to this post | posted 24 Feb, 2016 14:45

DanRussell

Joseph Ross
What do the X's mean? You have to mentally scoot the top line over a few spaces to line it up properly, but even still it's interesting that it recognizes some of the Xs as an identity to the target and some not. I've never seen this before. This is from LilDestine, in the product from the ORF that DNA Master calls starting at bp9002. It's a tail protein according to BLASTp at least.

Hi Joe,

Those Xs represent a "region of low complexity". What that basically means is that the amino acids there are quite similar to one another, or there are repetitive patterns, and as such they're bait for lots of meaningless alignments. Here's a link to NCBI's explanation. It's not something you should worry about, though!

–Dan

Posted in: DNA Master → Odd BLASTp alignment result

Link to this post \| posted 24 Feb, 2016 14:39
DanRussell	jparker jparker Hello, We are trying to BLAST in DNAM and are getting an "Integer Overflow" error message. This is a new one for us. Any thoughts? This was from trying to BLAST a single gene at 7pm PST, so shouldn't be PEAK hours. Thanks, Jordan Then we got this: Sending BLAST request… Waiting 74278080 seconds as requested… Hi Jordan, You can't just wait the 2.4 years for this result? Seriously, though, it looks like we're having the same issue. We'll let you know if we figure anything out. –Dan

Link to this post | posted 24 Feb, 2016 14:39

DanRussell

jparker
jparker
Hello,
We are trying to BLAST in DNAM and are getting an "Integer Overflow" error message. This is a new one for us. Any thoughts? This was from trying to BLAST a single gene at 7pm PST, so shouldn't be PEAK hours.
Thanks,
Jordan

Then we got this:
Sending BLAST request…
Waiting 74278080 seconds as requested…

Hi Jordan,

You can't just wait the 2.4 years for this result? smile

Seriously, though, it looks like we're having the same issue. We'll let you know if we figure anything out.

–Dan

Posted in: DNA Master → BLAST in DNAM

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