SEA-PHAGES | All posts created by DanRussell

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Link to this post \| posted 03 Jul, 2017 15:42
DanRussell	Hmmm…I was totally ready to say Chris is right, it's probably a 454 sequencing error, but here is the region in question in the assembly: The evidence for 6 Gs there is quite strong, and there are only a few reads that suggest only 5 Gs. That doesn't mean it's not truly 5 Gs, but I wouldn't feel comfortable changing the sequence on this evidence alone. I guess that means you should proceed as is? What do you think Welkin/Chris? –Dan

Link to this post | posted 03 Jul, 2017 15:42

Hmmm…I was totally ready to say Chris is right, it's probably a 454 sequencing error, but here is the region in question in the assembly:

The evidence for 6 Gs there is quite strong, and there are only a few reads that suggest only 5 Gs. That doesn't mean it's not truly 5 Gs, but I wouldn't feel comfortable changing the sequence on this evidence alone.

I guess that means you should proceed as is? What do you think Welkin/Chris?

–Dan

Posted in: Gene or not a Gene → Gene split in 2

Link to this post \| posted 25 Apr, 2017 19:26
DanRussell	Summer Research Opportunity Next-generation Fluorescent Reporter Mycobacteriophages The Jacobs laboratory has innovative and multifaceted studies on the biology of Mycobacterium tuberculosis and its phages. We are seeking undergraduates who have taken the SEA-PHAGES course to work on an exciting project to generate next-generation fluorescent reporter mycobacteriophages. We have previously shown that fluorescent reporter mycobacteriophages can be used to rapidly assess drug susceptibilities of Mycobacterium tuberculosis cells in culture or directly from sputum samples (Jain et al., 2012 Journal of Clinical Micro. 50:1362-9). Recently, we have developed dual reporter mycobacteriophages that can be used to identify M. tuberculosis persister cells, a subpopulation of cells in a culture that are drug tolerant (Jain et al., 2016 mBio. 7 e01023-16). The summer program will focus on generating improved versions of reporter mycobacteriophages (greater sensitivity, shelf-life etc.). This experience will help students explore nuances of molecular biology and the scientific method. Students with a basic background in biology, recombinant DNA technology, and phage biology would be ideally suited for this project. The students will not need to work with virulent M. tuberculosis strains as we have developed Biosafety Level 2 strains for this project. The Jacobs Lab is located in the Price Translational Research Center at the Albert Einstein College of Medicine, 1301 Morris Park Avenue, Bronx, NY. Einstein is near the Bronx Zoo and the New York Botanical Gardens (both ideal phage hunting areas!). The position will come with an stipend of $11,000 for 3 months. If interested, please contact Dr. William R. Jacobs at jacobsw@hhmi.org Lab webpage: http://williamrjacobs.org

Link to this post | posted 25 Apr, 2017 19:26

DanRussell

Summer Research Opportunity

Next-generation Fluorescent Reporter Mycobacteriophages

The Jacobs laboratory has innovative and multifaceted studies on the biology of Mycobacterium tuberculosis and its phages. We are seeking undergraduates who have taken the SEA-PHAGES course to work on an exciting project to generate next-generation fluorescent reporter mycobacteriophages.

We have previously shown that fluorescent reporter mycobacteriophages can be used to rapidly assess drug susceptibilities of Mycobacterium tuberculosis cells in culture or directly from sputum samples (Jain et al., 2012 Journal of Clinical Micro. 50:1362-9). Recently, we have developed dual reporter mycobacteriophages that can be used to identify M. tuberculosis persister cells, a subpopulation of cells in a culture that are drug tolerant (Jain et al., 2016 mBio. 7 e01023-16).

The summer program will focus on generating improved versions of reporter mycobacteriophages (greater sensitivity, shelf-life etc.). This experience will help students explore nuances of molecular biology and the scientific method. Students with a basic background in biology, recombinant DNA technology, and phage biology would be ideally suited for this project. The students will not need to work with virulent M. tuberculosis strains as we have developed Biosafety Level 2 strains for this project.

The Jacobs Lab is located in the Price Translational Research Center at the Albert Einstein College of Medicine, 1301 Morris Park Avenue, Bronx, NY. Einstein is near the Bronx Zoo and the New York Botanical Gardens (both ideal phage hunting areas!).

The position will come with an stipend of $11,000 for 3 months.

If interested, please contact Dr. William R. Jacobs at jacobsw@hhmi.org
Lab webpage: http://williamrjacobs.org

Posted in: General Message Board → 2017 Summer Opportunity at Albert Einstein College of Medicine

Link to this post \| posted 24 Apr, 2017 16:18
DanRussell	Hi Sangha, From looking at the DNA Master file, I think that the longer of these two (which overlaps a lot of other tRNAs) is just a miscall. You can safely delete that one. The 425 bp one, however, is probably a tmRNA, and should be called. –Dan

Posted in: Gene or not a Gene → C1 phage

Link to this post \| posted 12 Apr, 2017 14:38
DanRussell	Shallee Page The last couple of days, I can't open the Lawrence Lab web page to download DNA master… Hi Shallee, This happens from time to time. Looks like the server has been reset and is working now. –Dan

Posted in: DNA Master → DNA Master failed update

Link to this post \| posted 04 Apr, 2017 17:44
DanRussell	Hi Nancy, These are probably tRNA genes, which don't appear in Phamerator (yet!). So for those you'll have to follow some of the tRNA guidelines rather than Starterator, Phamerator, etc. –Dan

Posted in: Phamerator → Missing Genes in Phamerator Ading_draft

Link to this post \| posted 28 Mar, 2017 14:29
DanRussell	Hi Victoria, If Phamerator ever prompts you for a password, it should just be: "phage". If that doesn't work, something else has gone wrong! –Dan

Posted in: SEA-PHAGES Virtual Machine → No Ubuntu 64-bit option when installing 2017 VM on Windows

Link to this post \| posted 02 Mar, 2017 20:27
DanRussell	Hi Nikki, Glad it worked. Definitely shutting down the VM or closing your computer while Phamerator's running/doing things can cause problems. I'd always advise to close Phamerator before shutting anything else down. –Dan

Posted in: Phamerator → Locked out of Phamerator

Link to this post \| posted 01 Mar, 2017 15:39
DanRussell	Hi Nikki, Did you try "phage" for the password? If phamerator ever wants a password, that's the one. If that doesn't help, Steve recently answered a similar question via email, so I'm going to copy his response here: It sounds like one of two things: your virtual machine is unable to access the internet your phamerator configuration file has become corrupted You can test the first one by opening a browser in the virtual machine and trying to load any website. If that doesn’t work, you can usually solve the problem by rebooting the virtual machine or toggling the “enable networking” setting (turn off and then back on) from the dropdown menu near the top-right of your Ubuntu desktop. If that’s not the problem, I suggest that you move the Phamerator configuration file and allow Phamerator to recreate a default file: Steps to do this: Reboot the Virtual Machine Login as whichever account (seafaculty or seastudent) you prefer to use. (If you use both accounts, you will need to complete these steps logged in as each user.) Make sure Phamerator is NOT running. Open the terminal (click the Ubuntu “Dash” icon in the top-left corner, type “terminal” and hit the <enter> key) Paste in the following command: `mv ~/.phamerator/phamerator.conf ~/Desktop` Start Phamerator. You may need to update server to: http://phamerator.webfactional.com/databases_Hatfull and database to: Actino_Draft If prompted for a password, use: phage If everything appears to be in working order, you can delete the phamerator.conf file that is on your desktop. –Dan Edited 01 Mar, 2017 15:40

Link to this post | posted 01 Mar, 2017 15:39

DanRussell

Hi Nikki,

Did you try "phage" for the password? If phamerator ever wants a password, that's the one.

If that doesn't help, Steve recently answered a similar question via email, so I'm going to copy his response here:

It sounds like one of two things:
your virtual machine is unable to access the internet
your phamerator configuration file has become corrupted

You can test the first one by opening a browser in the virtual machine and trying to load any website. If that doesn’t work, you can usually solve the problem by rebooting the virtual machine or toggling the “enable networking” setting (turn off and then back on) from the dropdown menu near the top-right of your Ubuntu desktop.

If that’s not the problem, I suggest that you move the Phamerator configuration file and allow Phamerator to recreate a default file:

Steps to do this:
Reboot the Virtual Machine
Login as whichever account (seafaculty or seastudent) you prefer to use. (If you use both accounts, you will need to complete these steps logged in as each user.)
Make sure Phamerator is NOT running.
Open the terminal (click the Ubuntu “Dash” icon in the top-left corner, type “terminal” and hit the <enter> key)
Paste in the following command:
mv ~/.phamerator/phamerator.conf ~/Desktop
Start Phamerator. You may need to update server to: http://phamerator.webfactional.com/databases_Hatfull and database to: Actino_Draft
If prompted for a password, use: phage
If everything appears to be in working order, you can delete the phamerator.conf file that is on your desktop.

–Dan

Edited 01 Mar, 2017 15:40

Posted in: Phamerator → Locked out of Phamerator

Link to this post \| posted 09 Feb, 2017 15:32
DanRussell	Note that there's also a little document on using Inkscape with Phamerator maps that came out of the Faculty Retreat last year: http://seaphages.org/faculty/information/#modifications http://seaphages.org/media/docs/UsingInkscapeToEditPhameratorMaps.pdf –Dan

Posted in: Phamerator → Printing phamerator maps

Link to this post \| posted 07 Feb, 2017 16:39
DanRussell	Hi Joe, As for the BLASTing, you could try an intermediate approach between all-genes and one-at-a-time. Welkin made a video about how to BLAST a batch of genes in DNA Master, so you could try chunks of 10 for example. Batch BLASTing in DNA Master As to the E-value, those might just be a result of having a less-common cluster of phage this time around. If you had a new Singleton, you'd expect to see some genes with not-good BLAST hits. Cluster L3s are not that common (only 4 in GenBank, I believe), so it's totally possible that those are "new" genes. Check them out in Phamerator and see if they're orphams. (And an e-value of 1 just means that you'd expect about 1 hit this good against a database this size by random chance…meaning it is indeed a dubious result.) –Dan

Link to this post | posted 07 Feb, 2017 16:39

DanRussell

Hi Joe,

As for the BLASTing, you could try an intermediate approach between all-genes and one-at-a-time. Welkin made a video about how to BLAST a batch of genes in DNA Master, so you could try chunks of 10 for example.

Batch BLASTing in DNA Master

As to the E-value, those might just be a result of having a less-common cluster of phage this time around. If you had a new Singleton, you'd expect to see some genes with not-good BLAST hits. Cluster L3s are not that common (only 4 in GenBank, I believe), so it's totally possible that those are "new" genes. Check them out in Phamerator and see if they're orphams.

(And an e-value of 1 just means that you'd expect about 1 hit this good against a database this size by random chance…meaning it is indeed a dubious result.)

–Dan

Posted in: DNA Master → BLASTing whole genome with "secure" connection

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