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Recent Activity
All posts created by DanRussell
Link to this post | posted 08 Mar, 2024 00:32 | |
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Way back in our "60 phage paper", we grouped phages into clusters based on > 50% nucleotide similarity. Of course, exactly what "50% nucleotide similarity" meant depended on which metrics in particular you looked at, so we used several different ones. You can read about them in the paper. More recently, we've moved to comparing genes rather than nucleotides, and have used ~35% Gene Content Similarity to put phages into clusters. Now, we're probably moving towards using a metric called Protein Equivalence Quotient to cluster phages. It's an ongoing process, and there is no "right" answer and phages will always challenge us by not neatly fitting into bins. PhamClust paper There have been a few groups who have looked at geography, and though there doesn't seem to be any high-level correlation between geography and type of phages found, some subclusters or even genes have only been found in certain geographical areas. –Dan |
Posted in: Phage Biology → Phage Clustering
Link to this post | posted 13 Feb, 2024 14:57 | |
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eagodin Hi Liz, Just to be clear, the sequences were correct in the sense that all the bases were right. The change was just where Base 1 was, and duplicating a portion of the genome. (Not changing any individual bases or anything.) So everything should be fine/comparable, including the original annotations of those complete ones, but numbers will have changed. –Dan |
Posted in: Phamerator → Cluster FC in Phamerator
Link to this post | posted 08 Feb, 2024 19:31 | |
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Hi Nancy, Can you post the file here perhaps? Thanks, –Dan |
Posted in: DNA Master → Error when opening FASTA file
Link to this post | posted 10 Jan, 2024 21:38 | |
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jcaoyao@gmail.com Right, it's definitely more complicated than that! (At least for us at Pitt.) |
Posted in: Mycobacterium → Legal statement
Link to this post | posted 10 Jan, 2024 21:18 | |
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Hi Juan Carlos, Here in the Hatfull Lab at the University of Pittsburgh, all of our clinical M. abscessus isolates are classified as BSL-2, and for good reason. Sometimes an apparently "healthy human" may have undiagnosed or non-obvious issues, and treating an opportunistic pathogen as "harmless" is dangerous. As for the "ultimate, legal, foolproof" statement, that probably doesn't exist. BSL guidelines are set by your institution, and we at Pitt follow guidelines set by Pitt, the CDC, NIH, strain collections, etc. Different schools, countries, or organizations may have different rules, but we always expect all SEA-PHAGES schools to abide by appropriate BSL regulations in their region. We've had real safety concerns recently, as some SEA-PHAGES schools have tried phagehunting on bacteria they've isolated from the environment. While this offer a different phage yield, allowing students to work with an unknown bacterium and treating it as BSL-1 is not endorsed by the SEA-PHAGES program! –Dan |
Posted in: Mycobacterium → Legal statement
Link to this post | posted 03 Nov, 2023 16:47 | |
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Hi SEA-PHAGES faculty folks, We got the following message and wanted to pass it on to you in case you're looking for potential summer employment. "The Summer Science Program recently designed a program in bacterial genomics where participants evolve a BSL1 bacteria (V. natriegens) to tolerate ever-increasing levels of antibiotics. After the evolution and Illumina sequencing our participants assemble the genome and try to identify putative beneficial mutations. We are looking for faculty to lead the micro and the bioinformatics sides, and Phage Hunters seemed like a good place to find faculty." Details on their employment page: https://summerscience.org/employment/ –Dan |
Posted in: General Message Board → Summer Faculty Job Opportunity
Link to this post | posted 19 Jul, 2023 14:35 | |
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jcaoyao@gmail.com Hi, you can try opening a terminal and running this command:
If that doesn't work, I'd suggest asking the internet! –Dan |
Link to this post | posted 06 Jun, 2023 15:45 | |
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afreise Of course! Here you go: https://seaphages.org/forums/forum/222/ –Dan |
Posted in: Cluster-Specific Annotation Tips → Using This Forum
Link to this post | posted 27 Jan, 2023 18:06 | |
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From Eric Miller: We are still recruiting undergraduates for the forthcoming summer 2023 REEU BeeMORE (Bees and Microbes) program at NC State University. Our goal is to recruit as many students underrepresented in agriculture and science as possible; our participants are selected based on their motivation to learn and to make the most of our 9 week program. Undergraduates in their second or third year are preferred, with most of them coming from outside the NC State University community. Here is the link to our home page: https://harvest.cals.ncsu.edu/beemore/ On the web page there is a recent video describing the program, a flyer suitable for printing or sharing electronically, and a link to the brief application procedure. We expect to keep the application window open for a bit longer. The program is funded for at least the next four years. Please share broadly! Thank you for helping get the word out, to your students and to your colleagues. Post it on one of your web pages citing summer opportunities! Thank you and all the best, Eric |
Link to this post | posted 19 Jan, 2023 14:47 | |
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Hi Alison, Thanks. I asked because if they're the newer "M1" Macs, then we don't necessarily have a recommended way forward. (The chip architecture on the M1 Macs is different than the old Intel ones, and so VirtualBox will likely never work on M1s.) That said, if M1 is the issue, there's a big thread here on that: https://seaphages.org/forums/topic/5256/ –Dan |