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Center for Phage Technology at Texas A&M University
United States
Приєднався 6 лис 2018
Welcome to the Center for Phage Technology (CPT)! The CPT was established by the Texas A&M University System Board of Regents in 2010, as the first state-funded phage research institute in the United States. We are devoted to the study of phages for human health and agriculture, and give a strong focus on creating bioinformatics tools for phage genomics research. All the tools developed by CPT are publicly released to the scientific community via CPT Galaxy. cpt.tamu.edu/
2021 GCC Lightning Talk - Using custom Galaxy workflows to search for bacteriophage spanins
Dr. Jolene Ramsey describes a project using reproducible workflows to bioinformatically identify phage spanin proteins
This work is licensed under the Creative Commons Attribution-NonCommercial 4.0 International License.
Copyright © 2016-2021 Texas A&M University
cpt.tamu.edu/galaxy-pub
This work is licensed under the Creative Commons Attribution-NonCommercial 4.0 International License.
Copyright © 2016-2021 Texas A&M University
cpt.tamu.edu/galaxy-pub
Переглядів: 109
Відео
CPT GFF3 tool suite for manipulation, conversion and deposition of genome data
Переглядів 2613 роки тому
One of the strengths of Galaxy is the ability to chain analyses together into workflows, which saves user time and enhances reproducibility. A major barrier to workflow construction is the variability of tool input and output file formats; many tools produce outputs in bespoke formats that are not immediately usable in downstream processes. To alleviate this problem in the area of genome annota...
How to run PhageTerm tool in Galaxy
Переглядів 8463 роки тому
PhageTerm software is a tool to determine phage termini and packaging mode from high throughput sequences that rely on the random fragmentation of DNA (e.g. Illumina TruSeq, but NOT Nextera). This video is on how to run this tool in Galaxy. Please read the PhageTerm publication for more information. This work is licensed under the Creative Commons Attribution-NonCommercial 4.0 International Lic...
Annotating a gene in Apollo
Переглядів 3193 роки тому
This video demonstrates how to annotate a gene in Apollo. This work is licensed under the Creative Commons Attribution-NonCommercial 4.0 International License. Copyright © 2016-2021 Texas A&M University cpt.tamu.edu/galaxy-pub Music credit: Acoustic guitar arrangement for song by TRow soundcloud.com/megatrev Creative Commons - Attribution-ShareAlike 3.0 Unported- CC BY-SA 3.0 Free Download / St...
How to get amino acid and DNA sequence from a gene in Apollo
Переглядів 1233 роки тому
This video demonstrates how to get amino acid or DNA sequence associated with a gene in Apollo. This work is licensed under the Creative Commons Attribution-NonCommercial 4.0 International License. Copyright © 2016-2021 Texas A&M University cpt.tamu.edu/galaxy-pub Music credit: Acoustic guitar arrangement for song by TRow soundcloud.com/megatrev Creative Commons - Attribution-ShareAlike 3.0 Unp...
How to generate an annotation table for your annotated genome
Переглядів 1543 роки тому
This video demonstrates how to generate an annotation table for your annotated genome using the DNA FASTA and GFF3 files. This work is licensed under the Creative Commons Attribution-NonCommercial 4.0 International License. Copyright © 2016-2021 Texas A&M University cpt.tamu.edu/galaxy-pub Music credit: Acoustic guitar arrangement for song by TRow soundcloud.com/megatrev Creative Commons - Attr...
How to submit a bug report for a failed job in CPT Galaxy
Переглядів 573 роки тому
This video demonstrates how to view a failed job and and submit a bug report in CPT Galaxy. This work is licensed under the Creative Commons Attribution-NonCommercial 4.0 International License. Copyright © 2016-2021 Texas A&M University cpt.tamu.edu/galaxy-pub Music credit: Acoustic guitar arrangement for song by TRow soundcloud.com/megatrev Creative Commons - Attribution-ShareAlike 3.0 Unporte...
Cooperative bacteriophage genome annotation in the biologist-friendly Galaxy and Apollo platforms
Переглядів 3563 роки тому
2020 recorded talk by Jolene Ramsey for the virtual Bioinformatics Community Conference Galaxy track on the Center for Phage Technology Galaxy & Apollo annotation system.
Phage DNA extraction
Переглядів 1,3 тис.3 роки тому
In this video, Jay Clark demonstrates the DNA extraction protocol using the Promega Wizard DNA Clean-up kit (catalog # A7280). For written protocols, please go to cpt.tamu.edu/phage-links/phage-protocols/ This work is licensed under the Creative Commons Attribution-NonCommercial 4.0 International License. Copyright © 2016-2021 Texas A&M University cpt.tamu.edu
Making High Titer lysates
Переглядів 2 тис.3 роки тому
In this video, Dr. Burrowes demonstrates how to make and harvest solid media high titer lysates. For written protocols, please go to cpt.tamu.edu/phage-links/phage-protocols/ This work is licensed under the Creative Commons Attribution-NonCommercial 4.0 International License. Copyright © 2016-2021 Texas A&M University cpt.tamu.edu
Titering Phage - spot and whole plate methods
Переглядів 8 тис.3 роки тому
This video demonstrates the basics of making serial dilutions, spot titers, and whole plate titers. Analysis of results for each is also shown. For written protocols, please go to cpt.tamu.edu/phage-links/phage-protocols/ This work is licensed under the Creative Commons Attribution-NonCommercial 4.0 International License. Copyright © 2016-2021 Texas A&M University cpt.tamu.edu
Performing Streakate and Pickate
Переглядів 1,1 тис.3 роки тому
This video demonstrates the basic phage biology techniques for isolating phage plaques. For written protocols, please go to cpt.tamu.edu/phage-links/phage-protocols/ This work is licensed under the Creative Commons Attribution-NonCommercial 4.0 International License. Copyright © 2016-2021 Texas A&M University cpt.tamu.edu
How to start the CPT functional annotation workflow
Переглядів 2143 роки тому
This video demonstrates how to retrieve gene call data from Apollo to Galaxy, and how to run the functional workflow to conduct gene function annotation. This work is licensed under the Creative Commons Attribution-NonCommercial 4.0 International License. Copyright © 2016-2021 Texas A&M University cpt.tamu.edu/galaxy-pub Music from UA-cam Audio Library (No.9_Esther’s Waltz - Esther Abrami)
How to start the CPT structural annotation workflow
Переглядів 3013 роки тому
This video demonstrates how to upload your DNA sequence to a history, import and run the structural annotation workflow, and view the created Apollo record. This work is licensed under the Creative Commons Attribution-NonCommercial 4.0 International License. Copyright © 2016-2021 Texas A&M University cpt.tamu.edu/galaxy-pub Music credit: Acoustic guitar arrangement for song by TRow soundcloud.c...
How to call or delete gene, tRNA, and terminator in Apollo
Переглядів 1303 роки тому
This video demonstrates how to call (or delete) gene, tRNA and terminator in Apollo after you finish the structural annotation workflow. This work is licensed under the Creative Commons Attribution-NonCommercial 4.0 International License. Copyright © 2016-2021 Texas A&M University cpt.tamu.edu/galaxy-pub Music credit: Acoustic guitar arrangement for song by TRow soundcloud.com/megatrev Creative...
CPT functional workflow for phage genome annotation
Переглядів 2713 роки тому
CPT functional workflow for phage genome annotation
CPT structural workflow for phage genome annotation
Переглядів 3533 роки тому
CPT structural workflow for phage genome annotation
Introduction to the CPT Galaxy and WebApollo
Переглядів 9563 роки тому
Introduction to the CPT Galaxy and WebApollo
Can you tell me what the solution is to dilute the sample?
Hello, I got this message when I finished Error: you don't have a galaxy cookie. Please login to Galaxy first., but Im logged already
Thanks aloooot Please keep up the good work 🙌
Sir can u show isolation of phages from environmental samples as well ?
are you doing phage research too? I am doing the research from paddy field
I'm working on clinical aspect. Can you share me some protocols for geting plaque of phages n then isolating them ?
@@the11moon_ I do phage research from environmental samples
Very good presentation
I have a question I have proper plaques made of bacteriophage.Now my next step is to check it with some antiviral substance.So how do i use antiviral on the phage plaque ?
You can add the substance in the top agar while doing the double-layer agar technique. Add the co-culture to the molten agar, add the substance and pour over the hard agar
i look for a phage against Dermatitis digitalis do u know how to finde it. Is there literatur how to insult phages from nature?
Very well made and helpful thank you so much!
Hi, may I know where I can get this cell scraper? Thank you :)
Im currently doing phage therapy as my honours project and I'm pulling my hair out... My phage plaques seem to always be opaque, not completely transparent. Am I doing something wrong? Or could this mean that my phage are lysogenic, not lytic? Or something else?
mostly, lysogenic phages gives opaque plaques. but, do try Agar overlay at diffrent MOI. and observe that still plaques are opaque or clear
How did it go with your phage project?
@@Fidelanne great! I ended up isolating 3 novel phage, one of which was categorised as a Jumbo phage which I’m writing a paper on. I’m now doing a PhD but not in phage haha
@@KelliePixieAshton Good to know. Might as well do the same.
Can u please tell me how to get a proper curve for doing adsorption assay of one of my phages. i have been trying for long but I am not getting that curve and reduction of plaques after a time interval
Great !!
Great video, Actually I am facing problems in isolation and purification of single type of phage from waste sample. can you guide me? Sir if you have any protocol can you share it with me?
Hi ZAIUA MED, thanks for your question. Sorry we are late in our response, but if you check out our video on pickates and streakates here: ua-cam.com/video/jeRpyp5oLn0/v-deo.html, you should be able to get the method for picking a single plaque and isolating your phage from the others. This is the most commonly used method available. Our written protocols for this method and other basic phage biology methods can be found here: cpt.tamu.edu/phage-links/phage-protocols/.
Super helpful@@centerforphagetechnologyat5812
Great Video Thanks!
Great, glad you enjoyed it!
Thanks for video. I'm curious about DNA concentration. Did you determine concentration? thank you :)