SEA-PHAGES | All posts created by plymaler

Link to this post \| posted 07 Oct, 2025 23:25
plymaler	Hi all, Ouachita Baptist is hiring a tenure-track microbiologist to begin August 2026. The posting can be found here: https://obu.edu/about/hr/faculty-vacancies.php, and the priority application deadline is December 1, 2025. The faculty member is expected to teach the SEA-PHAGES bacteriophage discovery lab and allied health and majors’ microbiology courses. The faculty member will also provide undergraduate academic advising, supervise undergraduate research capstone and honors projects, and contribute to the overall academic environment of the department and the university. Ouachita Biology values hands-on education and the aptitude and inclination for engaging undergraduates in course-embedded undergraduate research experiences (CUREs) and/or individual mentored research is preferred. Let me (plymaler@obu.edu) or Nathan Reyna (reynan@obu.edu) know if you have questions or want more information. Ouachita Baptist University is a Christian liberal arts university with a robust Biology department. Our typical Biology major is a motivated, pre-medical-type student. We prioritize undergraduate research. We have CUREs in our General Biology I lab (phage and kombucha) and in our Microbiology, Cell Biology, and Genetics classes, and we mentor students in independent undergraduate research. Some of our faculty have extramural funding and we can provide a small amount of internal support. In addition to teaching in class and through research, we emphasize advising. Each student has a faculty advisor that they typically stay with until graduation. Faculty advisors support graduation requirements and do pre-professional advising. Ouachita Baptist University is a primarily undergraduate institution located in Arkadelphia, Arkansas, approximately 1 hour each from Little Rock, AR and Texarkana, TX, 3 hours from Memphis, and 4 hours each from Northwest Arkansas and Dallas. Edited 07 Oct, 2025 23:26

Link to this post | posted 07 Oct, 2025 23:25

Hi all,

Ouachita Baptist is hiring a tenure-track microbiologist to begin August 2026. The posting can be found here: https://obu.edu/about/hr/faculty-vacancies.php, and the priority application deadline is December 1, 2025.

The faculty member is expected to teach the SEA-PHAGES bacteriophage discovery lab and allied health and majors’ microbiology courses. The faculty member will also provide undergraduate academic advising, supervise undergraduate research capstone and honors projects, and contribute to the overall academic environment of the department and the university. Ouachita Biology values hands-on education and the aptitude and inclination for engaging undergraduates in course-embedded undergraduate research experiences (CUREs) and/or individual mentored research is preferred.

Let me (plymaler@obu.edu) or Nathan Reyna (reynan@obu.edu) know if you have questions or want more information.

Ouachita Baptist University is a Christian liberal arts university with a robust Biology department. Our typical Biology major is a motivated, pre-medical-type student. We prioritize undergraduate research. We have CUREs in our General Biology I lab (phage and kombucha) and in our Microbiology, Cell Biology, and Genetics classes, and we mentor students in independent undergraduate research. Some of our faculty have extramural funding and we can provide a small amount of internal support. In addition to teaching in class and through research, we emphasize advising. Each student has a faculty advisor that they typically stay with until graduation. Faculty advisors support graduation requirements and do pre-professional advising.

Ouachita Baptist University is a primarily undergraduate institution located in Arkadelphia, Arkansas, approximately 1 hour each from Little Rock, AR and Texarkana, TX, 3 hours from Memphis, and 4 hours each from Northwest Arkansas and Dallas.

Edited 07 Oct, 2025 23:26

Posted in: General Message Board → Tenure track Microbiology faculty position at Ouachita Baptist University in Arkansas

Link to this post \| posted 02 Sep, 2025 17:30
plymaler	Hi all, I have some previously-made, autoclaved PYCa broth, and I'm wondering if I can use it to extract smeg phage from a soil sample and then enrich. Will M. smegmatis grow in PYCa? Thank you, Ruth

Posted in: Phage Discovery/Isolation → grow smeg on PYCa

Link to this post \| posted 29 Sep, 2022 01:05
plymaler	Hi all, I am trying to use PhamNexus in the 2020 SEA VM. It asks me what database I want to use. I choose one and click "yes" when asked if I want to check the Hatfull server for the newest database version. Then, I am asked for the mySQL login info, which I do not know. Can someone tell me the login info, or if I need to change a setting in the SEA VM? I previously used this installation of the SEA VM for flatfile checking and that worked okay. Thank you!

Link to this post | posted 29 Sep, 2022 01:05

plymaler

Hi all,
I am trying to use PhamNexus in the 2020 SEA VM. It asks me what database I want to use. I choose one and click "yes" when asked if I want to check the Hatfull server for the newest database version. Then, I am asked for the mySQL login info, which I do not know. Can someone tell me the login info, or if I need to change a setting in the SEA VM? I previously used this installation of the SEA VM for flatfile checking and that worked okay.

Thank you!

Posted in: Bioinformatic Tools and Analyses → PhamNexus on SEA-VM

Link to this post \| posted 02 Feb, 2022 22:44
plymaler	I haven't made it to guest additions, as I ran into an error when I tried to start the SEA VM. I downloaded and unzipped the 2017 SEA VM, put it here, /home/ruth/VirtualBox VMs/SEAVM_2017.vmdk, and followed the setup directions from https://seaphages.org/software/virtualmachine/. When I started the VM, I got this error (attached screenshot). 18Kb

Posted in: SEA-PHAGES Virtual Machine → Installing SEA VM on Linux machine

Link to this post \| posted 01 Feb, 2022 22:29
plymaler	Great! I have VirtualBox installed, and am not sure whether to download the Windows or Mac SEA VM from seaphages.org. 163Kb

Posted in: SEA-PHAGES Virtual Machine → Installing SEA VM on Linux machine

Link to this post \| posted 31 Jan, 2022 22:02
plymaler	The Mac that I was using to run the SEA VM has aged out of updates and I have installed Linux Mint on the machine. Can I run the SEA VM on this operating system? I can install VirtualBox, but then need to choose between the Mac or Windows VM download. Thank you!

Posted in: SEA-PHAGES Virtual Machine → Installing SEA VM on Linux machine

Link to this post \| posted 15 Nov, 2018 02:38
plymaler	I am confused about the role of HHpred for genes of unknown function. Is it useful to record HHpred results that are a good match, but do not provide functional information? Or should HHpred only be recorded if it supports a specific function? For example, Parada_23 (19065 to 19505 (Forward)). The top HHpred result is to "DUF2744 ; Protein of unknown function", with a 98.5% probability and 73.2877% coverage. The probability and coverage seem good, but the "DUF" in DUF2744 stands for "domain of unknown function", so this result provides no functional data. Should I / my students mark / record this result in PECAAN / when doing annotations? Or, should HHpred results only be recorded if they have good probability and coverage AND indicate a specific function? (As a note, the second result is to an anti-sigma factor, with 39% probability and 21% coverage. PhagesDB and NCBI BLAST support a function of "minor tail protein".)

Link to this post | posted 15 Nov, 2018 02:38

plymaler

I am confused about the role of HHpred for genes of unknown function. Is it useful to record HHpred results that are a good match, but do not provide functional information? Or should HHpred only be recorded if it supports a specific function?

For example, Parada_23 (19065 to 19505 (Forward)). The top HHpred result is to "DUF2744 ; Protein of unknown function", with a 98.5% probability and 73.2877% coverage. The probability and coverage seem good, but the "DUF" in DUF2744 stands for "domain of unknown function", so this result provides no functional data. Should I / my students mark / record this result in PECAAN / when doing annotations? Or, should HHpred results only be recorded if they have good probability and coverage AND indicate a specific function?

(As a note, the second result is to an anti-sigma factor, with 39% probability and 21% coverage. PhagesDB and NCBI BLAST support a function of "minor tail protein".)

Posted in: Functional Annotation → marking HHpred for unknown function

Link to this post \| posted 07 Jul, 2018 17:09
plymaler	ThetaBob is an F4 phage. ThetaBob_107 has good HHPred matches to both glycosyltransferases and methyltransferases; screenshots of the HHPred output are attached. A combined glycosyltransferase/methytransferase function is not on the approved function list and so I am not sure how to identify the function of this protein. It does not seem to lean one way or the other. ThetaBob_107 is currently in pham 3147 with 9 other non-draft proteins, all in F phage. Avani_105, Jabbawokkie_106, Zapner_106, WillSterrel_99, Llama_108, and Demsculpinboyz_115 are all labeled as glycosyltransferase/methyltransferase. Che9d_109 and Yoshi_114 are labeled as glycosyl transferase. Che8_108 is unlabeled. Can glycosyltransferase/methytransferase be added an approved function? If not, what is the recommendation for how to label ThetaBob_107? Thanks! 352Kb

Link to this post | posted 07 Jul, 2018 17:09

plymaler

ThetaBob is an F4 phage. ThetaBob_107 has good HHPred matches to both glycosyltransferases and methyltransferases; screenshots of the HHPred output are attached. A combined glycosyltransferase/methytransferase function is not on the approved function list and so I am not sure how to identify the function of this protein. It does not seem to lean one way or the other.

ThetaBob_107 is currently in pham 3147 with 9 other non-draft proteins, all in F phage. Avani_105, Jabbawokkie_106, Zapner_106, WillSterrel_99, Llama_108, and Demsculpinboyz_115 are all labeled as glycosyltransferase/methyltransferase. Che9d_109 and Yoshi_114 are labeled as glycosyl transferase. Che8_108 is unlabeled.

Can glycosyltransferase/methytransferase be added an approved function? If not, what is the recommendation for how to label ThetaBob_107?

Thanks!

Posted in: Request a new function on the SEA-PHAGES official list → methyltransferase/glycosyltransferase

Link to this post \| posted 05 Jul, 2018 17:18
plymaler	Hi all, I am annotating ThetaBob, an F4 phage. ThetaBob_32 and 33 have been labeled Lysin A and Lysin B, respectively. ThetaBob_35 (stop 28491) is in pham 48862, and seven of the eight other members of this pham are marked as holins. ThetaBob_35 has no transmembrane domains. There are five other F phage with members of this pham marked as holins–Avani_37, Che9D_37, Demsculpinboyz_38, Jabbawokkie_40, Zapner_39–none of these proteins have transmembrane domains. There is sixth F phage with a gene in his pham–Yoshi_39. Yoshi_39 is marked as NKF, and no holin has been identified in Yoshi. There are two DP phage with members of this pham marked as holins–Ronaldo_64 and Fryberger_61–both each have one transmembrane domain. ThetaBob_38 has four transmembrane domains, but is well after the lysin genes. HHPred analysis shows a pfam match to E. coli holins in the last quarter of ThetaBob_38. My plan is to mark ThetaBob_35 as NKF, not as a holin, and to mark ThetaBob_38 as a membrane protein. Thanks for your thoughts!

Link to this post | posted 05 Jul, 2018 17:18

plymaler

Hi all,
I am annotating ThetaBob, an F4 phage. ThetaBob_32 and 33 have been labeled Lysin A and Lysin B, respectively.
ThetaBob_35 (stop 28491) is in pham 48862, and seven of the eight other members of this pham are marked as holins.
ThetaBob_35 has no transmembrane domains. There are five other F phage with members of this pham marked as holins–Avani_37, Che9D_37, Demsculpinboyz_38, Jabbawokkie_40, Zapner_39–none of these proteins have transmembrane domains. There is sixth F phage with a gene in his pham–Yoshi_39. Yoshi_39 is marked as NKF, and no holin has been identified in Yoshi.
There are two DP phage with members of this pham marked as holins–Ronaldo_64 and Fryberger_61–both each have one transmembrane domain.

ThetaBob_38 has four transmembrane domains, but is well after the lysin genes. HHPred analysis shows a pfam match to E. coli holins in the last quarter of ThetaBob_38.

My plan is to mark ThetaBob_35 as NKF, not as a holin, and to mark ThetaBob_38 as a membrane protein.

Thanks for your thoughts!

Posted in: Functional Annotation → holin with zero transmembrane domains in F cluster phage?

Link to this post \| posted 16 Jun, 2016 21:13
plymaler	Hi all, I compiled a list of bioinformatic software based on this year's symposium and previous meetings. It can be found at https://docs.google.com/spreadsheets/d/15dToev8nCF_sZMfuYmQo-uKat05m-CMwKsLQi3XGDA8/edit?usp=sharing and attached. 84Kb

Posted in: Annotation → List of bioinformatic software

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