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Link to this post \| posted 24 Mar, 2016 17:58
GregFrederick@letu.edu	I realized I put this in the wrong place… But I also just figured out that phamerator is capable of the Pham circles. Any thoughts on Phylogenetic trees?

Posted in: Papers → Pham and Phylogenetic analysis software

Link to this post \| posted 23 Mar, 2016 14:15
GregFrederick@letu.edu	Which softwares are best for producing Pham circles and Phylogenetic trees like those depicted in this reference? https://www.researchgate.net/figure/250926373_fig13_A-B-Pham-circles-for-phams-3687-A-and-6944-B-Phage-names-are-organized-by Thanks for your suggestions. Greg

Posted in: Papers → Pham and Phylogenetic analysis software

Link to this post \| posted 07 Mar, 2016 15:36
GregFrederick@letu.edu	Thanks guys!

Posted in: Phamerator → Analyze our near finished sequence in Phamerator???

Link to this post \| posted 04 Mar, 2016 17:48
GregFrederick@letu.edu	Thank you for all that info! GF

Posted in: Starterator → Starterter Analysis of our nearly finished sequence

Link to this post \| posted 03 Mar, 2016 23:30
GregFrederick@letu.edu	So are CDDs the number that is associated with the features in Phamerator? (Not the number hovering above each feature? What are these numbers, BTW?) Some of the yellow boxes have actual gene functions. So am I right that those do not have CDDs listed?

Posted in: Notes and Final Files → Conserved Domain ID in notes

Link to this post \| posted 03 Mar, 2016 22:56
GregFrederick@letu.edu	We are almost finished with the annotation of our first two genomes. We have added multiple genes that DNA Master did not call originally. QUESTION: Is there a way to manually input our nearly completed sequence into *Phamerator* to see what how it compares to similar sub-cluster phages? If so, how? If not, this would be a really nice feature to add. (I'm guessing the feature is already available. So please tell me how.) Thanks.

Link to this post | posted 03 Mar, 2016 22:56

GregFrederick@letu.edu

We are almost finished with the annotation of our first two genomes. We have added multiple genes that DNA Master did not call originally.

QUESTION: Is there a way to manually input our nearly completed sequence into Phamerator to see what how it compares to similar sub-cluster phages?

If so, how?

If not, this would be a really nice feature to add.

(I'm guessing the feature is already available. So please tell me how.)

Thanks.

Posted in: Phamerator → Analyze our near finished sequence in Phamerator???

Link to this post \| posted 03 Mar, 2016 22:52
GregFrederick@letu.edu	We are almost finished with our annotation of our first two genomes. We have added multiple genes that DNA Master did not call originally. QUESTION: Is there a way to manually input our near completed sequence into Starterator to see what it thinks about the start codons we have chosen? If so, how? If not, this would be a really nice feature to add. (I'm guessing the feature is already available. So please tell me how.) Thanks.

Link to this post | posted 03 Mar, 2016 22:52

GregFrederick@letu.edu

We are almost finished with our annotation of our first two genomes. We have added multiple genes that DNA Master did not call originally.

QUESTION: Is there a way to manually input our near completed sequence into Starterator to see what it thinks about the start codons we have chosen?

If so, how?

If not, this would be a really nice feature to add.

(I'm guessing the feature is already available. So please tell me how.)

Thanks.

Posted in: Starterator → Starterter Analysis of our nearly finished sequence

Link to this post \| posted 24 Feb, 2016 15:26
GregFrederick@letu.edu	joyous726 We have several students isolating lysogens and following a protocol that is on phagesdb.org (http://phagesdb.org/media/workflow/protocols/pdfs/LysogenyProtocol_3.19.13.pdf). I was wondering if there was anything additional in the way of protocols or background info that might be helpful for us. In particular, we find steps 11 - 14 a little vague and imply some working microbiological knowledge that we're a little shaky on. While we like to encourage student independence in reading protocols, we would love to have some more resources to direct them to for help. I know that other faculty have had students create stable lysogens to do immunity experiments. Is there anything that any of you have that might be helpful for us in the way of resources, additional protocols, or advice? Any help is appreciated! DId you get any responses to these questions outside the forum? Were your students successful? I have some questions too. We found what I think is an interesting mutant that I would like to investigate further. My email address is GregFrederick@letu.edu if you would rather communicate through email. Thanks.

Link to this post | posted 24 Feb, 2016 15:26

GregFrederick@letu.edu

joyous726
We have several students isolating lysogens and following a protocol that is on phagesdb.org (http://phagesdb.org/media/workflow/protocols/pdfs/LysogenyProtocol_3.19.13.pdf). I was wondering if there was anything additional in the way of protocols or background info that might be helpful for us. In particular, we find steps 11 - 14 a little vague and imply some working microbiological knowledge that we're a little shaky on. While we like to encourage student independence in reading protocols, we would love to have some more resources to direct them to for help. I know that other faculty have had students create stable lysogens to do immunity experiments. Is there anything that any of you have that might be helpful for us in the way of resources, additional protocols, or advice?

Any help is appreciated!

DId you get any responses to these questions outside the forum?

Were your students successful? I have some questions too. We found what I think is an interesting mutant that I would like to investigate further.

My email address is GregFrederick@letu.edu if you would rather communicate through email. Thanks.

Posted in: Lysogeny/Immunity → Lysogeny experiment help

Link to this post \| posted 18 Feb, 2016 19:59
GregFrederick@letu.edu	One of our teams noticed this as they were annotating and brought it to my attention this morning. The stop codon is about midway in the gene compared to all the other finished A6 phage genomes. He noticed the obvious mis-alignment of the two "features" the stop produced. The second feature was called from the next in-frame start codon after the stop. When he started blasting the homology of both to different regions of the same gene popped out at him. On to the science question: I am I correct in understanding that if the gene for the "immunity repressor protein" is inactivated lysogenized cells should be super-infectable by another A6 phage when normally they would likely not be were a functional protein produced? Is there an easy experimental method available to test for the inactivation of the immunity repressor protein? Is this even remotely interesting? I phamerated all the finished A6 genomes and did not find any others with this interrupting stop codon. Do we know of any other cases with this protein is disruppted? Can you think of any other interesting experiments that might be useful to conduct with this phage or lysogenized cells? Thanks for helping me brainstorm how discovery of this point mutation might be utilized further. Thanks. Greg

Link to this post | posted 18 Feb, 2016 19:59

GregFrederick@letu.edu

One of our teams noticed this as they were annotating and brought it to my attention this morning. The stop codon is about midway in the gene compared to all the other finished A6 phage genomes. He noticed the obvious mis-alignment of the two "features" the stop produced. The second feature was called from the next in-frame start codon after the stop. When he started blasting the homology of both to different regions of the same gene popped out at him.

On to the science question: I am I correct in understanding that if the gene for the "immunity repressor protein" is inactivated lysogenized cells should be super-infectable by another A6 phage when normally they would likely not be were a functional protein produced?

Is there an easy experimental method available to test for the inactivation of the immunity repressor protein? Is this even remotely interesting? I phamerated all the finished A6 genomes and did not find any others with this interrupting stop codon. Do we know of any other cases with this protein is disruppted?

Can you think of any other interesting experiments that might be useful to conduct with this phage or lysogenized cells?

Thanks for helping me brainstorm how discovery of this point mutation might be utilized further. Thanks. Greg

Posted in: Lysogeny/Immunity → One of our draft phage genomes has a 'stop' in the middle of the immunity repressor gene.

Link to this post \| posted 18 Feb, 2016 19:51
GregFrederick@letu.edu	Lee Hughes GregFrederick@letu.edu Thanks Lee. I had forgotten about that possibility. But does that mean that DaVinci (see image above) and all the others that do not have the programmed frameshift called are wrong and should be corrected? My guess would be that there is an error in DaVinci. That is one that should probably be reviewed. Which others (that aren't drafts) didn't have the frameshift annotated? Lee I have to say I don't remember the names of the other phages. (Can I blame it on old age even though I don't like to use that card?) It's been more than a few days and a few genes examined since I was doing those Phamerator alignments. I'll try to pull up more of the subcluster into Phamerator in class this afternoon and let you know. Thanks. Edited 18 Feb, 2016 20:04

Link to this post | posted 18 Feb, 2016 19:51

GregFrederick@letu.edu

Lee Hughes
GregFrederick@letu.edu
Thanks Lee. I had forgotten about that possibility. But does that mean that DaVinci (see image above) and all the others that do not have the programmed frameshift called are wrong and should be corrected?

My guess would be that there is an error in DaVinci. That is one that should probably be reviewed. Which others (that aren't drafts) didn't have the frameshift annotated?

Lee

I have to say I don't remember the names of the other phages. (Can I blame it on old age even though I don't like to use that card?) It's been more than a few days and a few genes examined since I was doing those Phamerator alignments. I'll try to pull up more of the subcluster into Phamerator in class this afternoon and let you know. Thanks.

Edited 18 Feb, 2016 20:04

Posted in: DNA Master → LO: Designation Question

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