SEA-PHAGES | All posts created by DanRussell

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Link to this post \| posted 04 Feb, 2016 21:31
DanRussell	chumho Some DM did not show Figure 1.2 completely, the lower part was totally missed (see pdf attached) even we updated DM and restarted PC many times. What might be wrong? Thanks, Eric. Hi Eric, What is the build number of the computers having problems? To find this out, go to Help –> About. –Dan

Posted in: DNA Master → Local settings/New Features differed from Fig 1.2

Link to this post \| posted 04 Feb, 2016 20:10
DanRussell	Tamarah Adair Yesterday we tried this new version out in lab and I was able to BLAST. The newest version to the box account is at the following link: https://baylor.box.com/s/sct7ixend1d29cn5n7qjlbcfod98hyny Changes: Rebuilt wine bottler package based on wine bottler 1.8rc4 (needed for El Capitan support) Updated to current version of DNAMaster (5.22.23 dated 1/26/16) Awesome, Tammy. Thanks for doing this. Hopefully this new version will work for everyone. –Dan

Link to this post | posted 04 Feb, 2016 20:10

DanRussell

Tamarah Adair
Yesterday we tried this new version out in lab and I was able to BLAST. The newest version to the box account is at the following link:

https://baylor.box.com/s/sct7ixend1d29cn5n7qjlbcfod98hyny
Changes:
Rebuilt wine bottler package based on wine bottler 1.8rc4 (needed for El Capitan support)
Updated to current version of DNAMaster (5.22.23 dated 1/26/16)

Awesome, Tammy. Thanks for doing this. Hopefully this new version will work for everyone.

–Dan

Posted in: DNA Master → Running DNA Master on a Mac using Wine

Link to this post \| posted 04 Feb, 2016 15:04
DanRussell	Just FYI, everyone, Debbie and I Googled the "OLE" error you've been getting, and it seems like it's a WINE error. So that, along with Kristen's last post, would seem to indicate that there's nothing wrong with the latest DNA Master version per se, but perhaps there's an issue with the way it interacts with WINE.

Posted in: DNA Master → Running DNA Master on a Mac using Wine

Link to this post \| posted 03 Feb, 2016 14:48
DanRussell	saleadon Can you "overwhelm" Starterator? Analyzing one of our genes produced 351 tracks! The graph was incomplete: it only listed the first few start sites for just one of the tracks. The report appears to be useful, although it would be nice to see the graph. Thanks. Hey Steve, What was the gene and Pham number that this happened on? –Dan

Posted in: Phamerator → Tutorial on Phamerator and Starterator Use?

Link to this post \| posted 02 Feb, 2016 20:03
DanRussell	Lee Hughes Dan - I have a student who wants to install the VM on his computer. Can I get the link please? Thanks, Lee Just sent them to you. –Dan

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

Link to this post \| posted 27 Jan, 2016 20:45
DanRussell	cmageeney QUESTIONS: 1. Are both blasts really necessary? Both blast are important because they give you different data. The NCBI blast will give you all information while phagesdb blast will only give you actinobacter phages. You can however individually blast each gene product as you annotate in DNAmaster. I find this helpful for students since they can then make start site changes and re-blast, when necessary. What I typically do is set my personal file to blast overnight. I have never had a problem doing it that way then I have all the data needed. 2. What might the PhagesDB BLASTp turn up that the NCBI would not (archived phage genes, I suppose.)? phagedb is going to show all the blast hits in actinobacter phages. This may be useful if you are looking for other phages that are not in genbank yet. 3. What might the NCBI BLASTp turn up that the PhagesDB BLASTp would not? So far, they are identical. NCBI will turn up many additional results that phagesdb is not set for. These could be hits in bacterial species, other types of phages, such as coli phages. 4. HHPred returns completely different regional homologies. Is there a threshold, i.e. number of AAs in a string that might be of interest? We ask our students to use their best judgement about functional information here. I use 95% homology and e-values higher than 10^-5. This is not a hard rule but a good guideline to start with. 5. In HHPred if the query sequence is 150aa long and a homologous stretch of 18-20aa is return in say an "E. coli DNA Gyrase Inhibitor" can/should we ignore such short homologies? Take all information into consideration but use your best judgement. Hope this helps and anyone else that has information to answer these that I might have missed feel free to jump in. Nicely answered, Katie! Thanks. –Dan

Link to this post | posted 27 Jan, 2016 20:45

DanRussell

cmageeney
QUESTIONS:

1. Are both blasts really necessary?
Both blast are important because they give you different data. The NCBI blast will give you all information while phagesdb blast will only give you actinobacter phages. You can however individually blast each gene product as you annotate in DNAmaster. I find this helpful for students since they can then make start site changes and re-blast, when necessary. What I typically do is set my personal file to blast overnight. I have never had a problem doing it that way then I have all the data needed.

2. What might the PhagesDB BLASTp turn up that the NCBI would not (archived phage genes, I suppose.)?
phagedb is going to show all the blast hits in actinobacter phages. This may be useful if you are looking for other phages that are not in genbank yet.

3. What might the NCBI BLASTp turn up that the PhagesDB BLASTp would not? So far, they are identical.
NCBI will turn up many additional results that phagesdb is not set for. These could be hits in bacterial species, other types of phages, such as coli phages.

4. HHPred returns completely different regional homologies. Is there a threshold, i.e. number of AAs in a string that might be of interest?
We ask our students to use their best judgement about functional information here. I use 95% homology and e-values higher than 10^-5. This is not a hard rule but a good guideline to start with.

5. In HHPred if the query sequence is 150aa long and a homologous stretch of 18-20aa is return in say an "E. coli DNA Gyrase Inhibitor" can/should we ignore such short homologies?
Take all information into consideration but use your best judgement.

Hope this helps and anyone else that has information to answer these that I might have missed feel free to jump in.

Nicely answered, Katie! Thanks.

–Dan

Posted in: DNA Master → PhagesDB vs NCBI BLASTp results - the value of both?

Link to this post \| posted 27 Jan, 2016 20:39
DanRussell	Lee Hughes I just ignore the updates personally. I might change to the new version after a semester, but never during. Don't want to take any chances that things will get mucked up. I agree 100% with Lee here. Unless there's something that's not working (or if there's a new feature in the update that you MUST have), don't upgrade. –Dan

Posted in: SEA-PHAGES Virtual Machine → Oracle VB Updates - How often do you recommend students upgrade?

Link to this post \| posted 21 Jan, 2016 03:55
DanRussell	ksaville yep - it showed up now. I found Timmi and he wasn't trapped in a well. Thanks I never understood why Timmi was so interested in playing near wells all the time. Glad to hear he's safe and you've figured out the Phamerator issue! –Dan

Posted in: Phamerator → Databases and Alternate hosts

Link to this post \| posted 13 Jan, 2016 21:37
DanRussell	Kristen Butela Hi there Greg! Yes, I am currently still using WINE to run DNA Master. The great thing about WINE is that it really isn't a Windows emulator that requires a separate virtual machine-any WINE program can run on the native MacOS. From my understanding, WINE in combination with X11 provides a basic scaffold on the Mac on which Windows programs can run. All you need to do is to make sure that XQuartz/X11 (http://www.xquartz.org/) is installed on the computer (this permits WINE programs to function). Tamarah's link contains the entire DNA Master package. The Mac will treat this program as an app. Good luck, and let me know if you have any questions! Good point. I think that X11 used to be included by default on Mac OS X installations, up til about 10.6, but no longer is. You'll need to add it on newer versions of OS X, but that should be fairly painless using the link Kristen supplied. –Dan

Link to this post | posted 13 Jan, 2016 21:37

DanRussell

Kristen Butela
Hi there Greg! Yes, I am currently still using WINE to run DNA Master. The great thing about WINE is that it really isn't a Windows emulator that requires a separate virtual machine-any WINE program can run on the native MacOS. From my understanding, WINE in combination with X11 provides a basic scaffold on the Mac on which Windows programs can run. All you need to do is to make sure that XQuartz/X11 (http://www.xquartz.org/) is installed on the computer (this permits WINE programs to function). Tamarah's link contains the entire DNA Master package. The Mac will treat this program as an app. Good luck, and let me know if you have any questions!

Good point. I think that X11 used to be included by default on Mac OS X installations, up til about 10.6, but no longer is. You'll need to add it on newer versions of OS X, but that should be fairly painless using the link Kristen supplied.

–Dan

Posted in: DNA Master → Running DNA Master on a Mac using Wine

Link to this post \| posted 13 Jan, 2016 21:28
DanRussell	GregFrederick@letu.edu Tamarah Adair We are running DNA Master within the WINE configuration. The installer has been copied and you should be able to get to it from this link. https://baylor.box.com/s/295to06pr1cpztqiu2jn0h77iy3vkanz Our contact is in Student Technology Services. He installs the DNA Master on the Macs in the lab at the beginning of the spring semester. If there are updates he incorporates these. I'm sure he would be glad to answer any questions you might have. Hey Tammy. I'm not a Mac guy… I used one some 20 years ago… but it has been a while. Your link above still works. It leads to file called DNAMaster_5.22.19.dmg Is that an executable file on Mac OS10? Does it need to be extracted? Or opened in another program? Sorry for the newb questions! Thanks! Greg Hi Greg, The .dmg is the standard disk image format for Mac, meaning it's the format in which most Mac programs are downloaded now, so it'll be totally fine with all OSX versions, and you should just be able to double-click after downloading. –Dan

Link to this post | posted 13 Jan, 2016 21:28

DanRussell

GregFrederick@letu.edu
Tamarah Adair
We are running DNA Master within the WINE configuration.
The installer has been copied and you should be able to get to it from this link.
https://baylor.box.com/s/295to06pr1cpztqiu2jn0h77iy3vkanz

Our contact is in Student Technology Services. He installs the DNA Master on the Macs in the lab at the beginning of the spring semester. If there are updates he incorporates these. I'm sure he would be glad to answer any questions you might have.
Hey Tammy. I'm not a Mac guy… I used one some 20 years ago… but it has been a while.

Your link above still works. It leads to file called DNAMaster_5.22.19.dmg

Is that an executable file on Mac OS10? Does it need to be extracted? Or opened in another program? Sorry for the newb questions!

Thanks! Greg

Hi Greg,

The .dmg is the standard disk image format for Mac, meaning it's the format in which most Mac programs are downloaded now, so it'll be totally fine with all OSX versions, and you should just be able to double-click after downloading.

–Dan

Posted in: DNA Master → Running DNA Master on a Mac using Wine

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