SEA-PHAGES | All posts created by DanRussell

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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

Link to this post \| posted 18 Feb, 2016 16:00
DanRussell	GregFrederick@letu.edu Dan Russell Hi Greg, The coding potential looks sparse on the reverse strand in that region. Quick question: what are the other genomes where that reverse-strand gene is called? Are any (or all) of those still in "_Draft" form? –Dan Dan: I do not have the names in front of me. But when I looked at it with students the other day it appeared that all the hits were in the NCBI Blasts or in 'draft' genomes in the PHAGESBD database. I concluded that those in the NCBI Blast hits were probably "auto-annotated" and deposited without QC (possibly by another group). We determined it was not likely a "real" gene. But it is an incredibly long ORF. So that call was not entirely 'comfortable'. I did end up taking a quick look in Phamerator, and it seemed like the Final genomes all had removed that reverse-strand gene, while the Draft ones still had it. So probably dropping it is the way to go. –Dan

Link to this post | posted 18 Feb, 2016 16:00

DanRussell

GregFrederick@letu.edu
Dan Russell
Hi Greg,

The coding potential looks sparse on the reverse strand in that region.

Quick question: what are the other genomes where that reverse-strand gene is called? Are any (or all) of those still in "_Draft" form?

–Dan

Dan:

I do not have the names in front of me. But when I looked at it with students the other day it appeared that all the hits were in the NCBI Blasts or in 'draft' genomes in the PHAGESBD database.

I concluded that those in the NCBI Blast hits were probably "auto-annotated" and deposited without QC (possibly by another group). We determined it was not likely a "real" gene. But it is an incredibly long ORF. So that call was not entirely 'comfortable'.

I did end up taking a quick look in Phamerator, and it seemed like the Final genomes all had removed that reverse-strand gene, while the Draft ones still had it. So probably dropping it is the way to go.

–Dan

Posted in: Gene or not a Gene → Cluster G genes spanning the COS site

Link to this post \| posted 16 Feb, 2016 21:12
DanRussell	coomansr All, We have the same. Do you suggest just using the other 2 databases or selecting another as a third? Roy Hi Roy, I think just going with the two recommended databases is fine. –Dan

Posted in: Functional Annotation → HHPred databases

Link to this post \| posted 12 Feb, 2016 22:16
DanRussell	Hi all, If you've successfully set up the SEA VM, but are still struggling with DNA Master, you might be interested in giving this new approach a shot. It allows you to run DNA Master within the SEA VM itself. It should be emphasized that this is a beta test only and is only recommended if you're an intrepid type and not worried about potential hiccups. That said, this has a lot of potential to be the future of how SEA-PHAGES uses DNA Master, and so any feedback we get would be welcome. I'll post a link to the instructions for doing this. Please use this forum to document any issues with the installation and/or running of DNA Master within the VM. http://seaphages.org/media/docs/DNA_Master_on_SEAVM_instructions.docx (Big thanks to Kristen Butela, Tammy Adair, Keith Hutchison, and others who have been troubleshooting non-Windows DNA Master.) Thanks, –Dan Edited 12 Feb, 2016 22:21

Link to this post | posted 12 Feb, 2016 22:16

DanRussell

Hi all,

If you've successfully set up the SEA VM, but are still struggling with DNA Master, you might be interested in giving this new approach a shot. It allows you to run DNA Master within the SEA VM itself. It should be emphasized that this is a beta test only and is only recommended if you're an intrepid type and not worried about potential hiccups. That said, this has a lot of potential to be the future of how SEA-PHAGES uses DNA Master, and so any feedback we get would be welcome.

I'll post a link to the instructions for doing this. Please use this forum to document any issues with the installation and/or running of DNA Master within the VM.

http://seaphages.org/media/docs/DNA_Master_on_SEAVM_instructions.docx

(Big thanks to Kristen Butela, Tammy Adair, Keith Hutchison, and others who have been troubleshooting non-Windows DNA Master.)

Thanks,
–Dan

Edited 12 Feb, 2016 22:21

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

Link to this post \| posted 12 Feb, 2016 15:08
DanRussell	Hi Greg, The coding potential looks sparse on the reverse strand in that region. Quick question: what are the other genomes where that reverse-strand gene is called? Are any (or all) of those still in "_Draft" form? –Dan

Posted in: Gene or not a Gene → Cluster G genes spanning the COS site

Link to this post \| posted 12 Feb, 2016 14:58
DanRussell	andersonr24@gator.uhd.edu Is it possible to be emailed the SeaVM file? I am a student and I am trying to annotate, but unable to comlplete without this file. Thanks! andersonr24@gator.uhd.edu Yep, just sent them to you. –Dan

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

Link to this post \| posted 11 Feb, 2016 14:46
DanRussell	(Also, make sure you restart Phamerator once the database update is complete.)

Posted in: Phamerator → Seemingly "uneven" updating of Phamerator db

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