SEA-PHAGES | All posts created by DanRussell

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Link to this post \| posted 09 Feb, 2016 15:32
DanRussell	Veronique Delesalle I'm using HHPred tonight (Feb 7th) and can only see the databases pbd70_ and pfam_. There is no tigrfam_! Anybody knows what happened to that database? Thx, Veronique I noticed this as well, Véronique. I'm not sure why, but just wanted to confirm that it's not something about your computer or setup! –Dan

Posted in: Functional Annotation → HHPred databases

Link to this post \| posted 04 Feb, 2016 21:52
DanRussell	chumho Dan Russell 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 Version 5.22.5. Actually I had asked our IT to download and reinstall DNA Master again. It is working now. The current version is 5.22.23. But I'm confused why the 'update DNA Master' function didn't do the work. The most common problem with DNA Master is that it's not being run as an administrator. If not, then even when the update "completes", it won't really be updated. The best thing to do is to check that build number and see whether it's up-to-date or not. If not, then run an update and check the build number again. If it hasn't updated, then something else is wrong (like not running as an administrator). –Dan

Link to this post | posted 04 Feb, 2016 21:52

DanRussell

chumho
Dan Russell
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

Version 5.22.5. Actually I had asked our IT to download and reinstall DNA Master again. It is working now. The current version is 5.22.23. But I'm confused why the 'update DNA Master' function didn't do the work.

The most common problem with DNA Master is that it's not being run as an administrator. If not, then even when the update "completes", it won't really be updated. The best thing to do is to check that build number and see whether it's up-to-date or not. If not, then run an update and check the build number again. If it hasn't updated, then something else is wrong (like not running as an administrator).

–Dan

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

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

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