SEA-PHAGES | All posts created by kbutela

Link to this post \| posted 30 Aug, 2021 22:18
kbutela	It sounds like you are having the same FTP connection issues within DNA Master that we encountered over the summer (see https://seaphages.org/forums/topic/5155/?page=2). We were able to download DNA Master onto Windows 10, but we cannot get DNA Master to complete its update. When we try to update, we get a message that DNA Master is updating helper programs, and when this reaches 3%, we get the error message "FTP failure," and DNA Master isn't able to fully update itself. This results in limited functionality of the program. BLAST searches fail, but I'm not certain what else also fails since I haven't done extensive testing. The problem isn't with downloading DNA Master, the problem lies with DNA Master not being able to connect to the FTP site to update itself. We have been unable to solve this issue on our own.

Link to this post | posted 30 Aug, 2021 22:18

It sounds like you are having the same FTP connection issues within DNA Master that we encountered over the summer (see https://seaphages.org/forums/topic/5155/?page=2). We were able to download DNA Master onto Windows 10, but we cannot get DNA Master to complete its update. When we try to update, we get a message that DNA Master is updating helper programs, and when this reaches 3%, we get the error message "FTP failure," and DNA Master isn't able to fully update itself. This results in limited functionality of the program. BLAST searches fail, but I'm not certain what else also fails since I haven't done extensive testing.

The problem isn't with downloading DNA Master, the problem lies with DNA Master not being able to connect to the FTP site to update itself. We have been unable to solve this issue on our own.

Posted in: DNA Master → DNA Master Issue

Link to this post \| posted 28 Jun, 2021 16:45
kbutela	Thanks Christian! I have the file checker running on my Mac now and I was able to successfully run it with a test genome. I have attached the original instructions file with my edits and screenshots. I encountered a few more hiccups but I was able to solve them, so I put in my workarounds and triggered error messages in the document on the steps where the problems occurred. 250Kb

Posted in: Notes and Final Files → New File Checker for Mac

Link to this post \| posted 28 Jun, 2021 14:21
kbutela	Hi Christian- Thanks for this new set of instructions! Unfortunately I still get stuck fairly early in the process. When I update my bash_profile file with `nano ~/.bash_profile export $PATH=’$PATH:/usr/local/mysql/bin’` I get this error message: `/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin=$PATH:/usr/local/mysql/bin': not a valid identifier` I am unsure how to proceed. I can try to create a new bash_profile file but other than this I'm out of ideas. UPDATE: I looked on some help forums and they suggested changing `export $PATH=’$PATH:/usr/local/mysql/bin’` to `export PATH=’$PATH:/usr/local/mysql/bin’` This seems to have solved the problem and I am proceeding with the install. I am going to edit a version of the instructions as I go. Edited 28 Jun, 2021 14:36

Link to this post | posted 28 Jun, 2021 14:21

kbutela

Hi Christian-

Thanks for this new set of instructions! Unfortunately I still get stuck fairly early in the process. When I update my bash_profile file with

nano ~/.bash_profile
export $PATH=’$PATH:/usr/local/mysql/bin’

I get this error message:

/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin=$PATH:/usr/local/mysql/bin': not a valid identifier

I am unsure how to proceed. I can try to create a new bash_profile file but other than this I'm out of ideas.

UPDATE: I looked on some help forums and they suggested changing

export $PATH=’$PATH:/usr/local/mysql/bin’

export PATH=’$PATH:/usr/local/mysql/bin’

This seems to have solved the problem and I am proceeding with the install. I am going to edit a version of the instructions as I go.

Edited 28 Jun, 2021 14:36

Posted in: Notes and Final Files → New File Checker for Mac

Link to this post \| posted 25 Jun, 2021 20:26
kbutela	Does anyone have instructions for installing the new flat file checker on MacOS? I'm trying from the pdm_utils page but keep hitting a lot of roadblocks with things not working as described.

Posted in: Notes and Final Files → New File Checker for Mac

Link to this post \| posted 24 Jun, 2021 20:14
kbutela	Update-Dan is working on troubleshooting the issue with DNA Master on Windows 10 machines. For now, it appears that new installations are problematic but existing installations are able to successfully update and have full functionality. Depending on the nature of the problem, Jeffrey Lawrence may need to modify some settings in DNA Master. I will keep everyone updated on the status of this issue.

Link to this post | posted 24 Jun, 2021 20:14

kbutela

Update-Dan is working on troubleshooting the issue with DNA Master on Windows 10 machines. For now, it appears that new installations are problematic but existing installations are able to successfully update and have full functionality. Depending on the nature of the problem, Jeffrey Lawrence may need to modify some settings in DNA Master. I will keep everyone updated on the status of this issue.

Posted in: DNA Master → DNA master server down?

Link to this post \| posted 21 Jun, 2021 17:31
kbutela	If the phams in question aren't orphams, I think the best choice would be to wait a few days and try again to access the reports. Another option would be to have the students clear their browser cache and cookies regularly just in case their browsers are going to outdated links and are showing the error message instead of the regular Starterator report. Here is a link to my video on an intro to Starterator and how to access reports both from PECAAN and from PhagesDB. Hope it helps! Start Site Evaluation Tools: Starterator

Link to this post | posted 21 Jun, 2021 17:31

kbutela

If the phams in question aren't orphams, I think the best choice would be to wait a few days and try again to access the reports. Another option would be to have the students clear their browser cache and cookies regularly just in case their browsers are going to outdated links and are showing the error message instead of the regular Starterator report.

Here is a link to my video on an intro to Starterator and how to access reports both from PECAAN and from PhagesDB. Hope it helps!

Start Site Evaluation Tools: Starterator

Posted in: Starterator → Pham not found in Starterator

Link to this post \| posted 21 Jun, 2021 17:07
kbutela	Hi Kathleen! Are your students accessing Starterator reports via PECAAN or directly through PhagesDB? If they are using PECAAN, I have a video demonstrating how to solve this issue. kcornely Greetings, all, I have a student doing a summer research project and she is annotating the phage Tarkin. There are a number of phams that are not found in Starterator. We've been checking the database regularly, and we can see that the data base number has been changing frequently, so we're assuming that Chris Schaffer is hard at work updating it. Should we wait for the updates or would you like us to send you the pham numbers for the phams that are missing Starterator reports? Thanks very much! Kathleen

Link to this post | posted 21 Jun, 2021 17:07

kbutela

Hi Kathleen! Are your students accessing Starterator reports via PECAAN or directly through PhagesDB? If they are using PECAAN, I have a video demonstrating how to solve this issue.

kcornely
Greetings, all,
I have a student doing a summer research project and she is annotating the phage Tarkin. There are a number of phams that are not found in Starterator. We've been checking the database regularly, and we can see that the data base number has been changing frequently, so we're assuming that Chris Schaffer is hard at work updating it. Should we wait for the updates or would you like us to send you the pham numbers for the phams that are missing Starterator reports?
Thanks very much!
Kathleen

Posted in: Starterator → Pham not found in Starterator

Link to this post \| posted 27 May, 2021 13:27
kbutela	In a previous post, Christian mentioned that there is a $40 paid program called CrossOver for Macs running Catalina and newer OS versions that permits you to use DNA Master on the Mac without a virtual machine. If there's enough interest, I can beta test the trial version later this summer. Edited 27 May, 2021 13:27

Posted in: DNA Master → Key Violation

Link to this post \| posted 13 May, 2021 15:14
kbutela	Hi all- I am working with phage Fitzgerald and wanted to follow up on Chris' proposal to add ribosome modulation factor to the approved functions database. Fitzgerald gp 14 (11299-11517) is 73 aa in length but is in a different pham than Gilgamesh gp 51. However, it aligns to the A chain of crystal structure 2JRM and 4V8G_CV, both of which are annotated as ribosome modulation factor in HHPred. Alignments are 98% probability with 60-70% coverage. I did an alignment of several BLAST results from this gene with the Escherichia coli RMF (see attached). There are 4 conserved residues that match up with the findings from E. coli RMF and other gammaproteobacteria (https://www.frontiersin.org/articles/10.3389/fmolb.2021.661691/full). Gilgamesh gp51 is annotated as ribosome modulation factor, but this function isn't on the approved list yet. Is this an okay term to use, or do we need more evidence? Edited 13 May, 2021 15:14 62Kb

Link to this post | posted 13 May, 2021 15:14

kbutela

Hi all-

I am working with phage Fitzgerald and wanted to follow up on Chris' proposal to add ribosome modulation factor to the approved functions database. Fitzgerald gp 14 (11299-11517) is 73 aa in length but is in a different pham than Gilgamesh gp 51. However, it aligns to the A chain of crystal structure 2JRM and 4V8G_CV, both of which are annotated as ribosome modulation factor in HHPred. Alignments are 98% probability with 60-70% coverage. I did an alignment of several BLAST results from this gene with the Escherichia coli RMF (see attached). There are 4 conserved residues that match up with the findings from E. coli RMF and other gammaproteobacteria (https://www.frontiersin.org/articles/10.3389/fmolb.2021.661691/full).

Gilgamesh gp51 is annotated as ribosome modulation factor, but this function isn't on the approved list yet. Is this an okay term to use, or do we need more evidence?

Edited 13 May, 2021 15:14

Posted in: Request a new function on the SEA-PHAGES official list → Ribosomal Modulation Factor

Link to this post \| posted 07 May, 2021 15:56
kbutela	I'd like some community input on how everyone is thinking about the call of Cas4 family exonuclease vs. RecE-like exonuclease. According to the approved functions list, we call RecB-like exonuclease/helicase if we can confidently identify both a helicase and an exonuclease domain present in the protein. Cas4 family exonuclease is called if we see alignments to the crystal structure 3H4R_A and to the PD-(D/E)XK nuclease superfamily (PF12705.7, among others) according to the functions list. It's a little more unclear on calling the RecE-like exonuclease. Presumably we should be looking for alignments to RecE crystal structures. I've been using this as a guide for my own annotations. Using Che9c_60 as a model for RecE-like exonuclease (from approved list), HHPred reveals matches to 3H4R_A and PF12705.7. Che9c_61 is called as a RecT-like ssDNA binding protein. There are no alignments to anything labeled as RecE. My question is: should we be calling RecE-like exonuclease for a gene that has the exonuclease only domains and is immediately upstream of a RecT-like ssDNA binding protein (regardless of hits to 3H4E_A and PD-(D/E)XK nuclease superfamilies), and reserve Cas4 family exonuclease for genes that are not immediately upstream or very close to a RecT-like ssDNA binding protein? My immediate thoughts are to use the presence of RecT as a guide to call RecE-like exonuclease, but I want to hear what you all think.

Link to this post | posted 07 May, 2021 15:56

kbutela

I'd like some community input on how everyone is thinking about the call of Cas4 family exonuclease vs. RecE-like exonuclease. According to the approved functions list, we call RecB-like exonuclease/helicase if we can confidently identify both a helicase and an exonuclease domain present in the protein. Cas4 family exonuclease is called if we see alignments to the crystal structure 3H4R_A and to the PD-(D/E)XK nuclease superfamily (PF12705.7, among others) according to the functions list. It's a little more unclear on calling the RecE-like exonuclease. Presumably we should be looking for alignments to RecE crystal structures. I've been using this as a guide for my own annotations.

Using Che9c_60 as a model for RecE-like exonuclease (from approved list), HHPred reveals matches to 3H4R_A and PF12705.7. Che9c_61 is called as a RecT-like ssDNA binding protein. There are no alignments to anything labeled as RecE.

My question is: should we be calling RecE-like exonuclease for a gene that has the exonuclease only domains and is immediately upstream of a RecT-like ssDNA binding protein (regardless of hits to 3H4E_A and PD-(D/E)XK nuclease superfamilies), and reserve Cas4 family exonuclease for genes that are not immediately upstream or very close to a RecT-like ssDNA binding protein? My immediate thoughts are to use the presence of RecT as a guide to call RecE-like exonuclease, but I want to hear what you all think.

Posted in: Functional Annotation → Refining the call for Cas4 family exonuclease vs. RecE-like exonuclease

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