Welcome to the forums at seaphages.org. Please feel free to ask any questions related to the SEA-PHAGES program. Any logged-in user may post new topics and reply to existing topics. If you'd like to see a new forum created, please contact us using our form or email us at info@seaphages.org.
Recent Activity
All posts created by DanRussell
Link to this post | posted 04 Jun, 2024 17:04 | |
---|---|
|
And another one from Roger Hendrix, from this paper:Comparative examination of [phage] genomes indicates that the hallmark of phage evolution is horizontal exchange of sequences. This is accomplished, first, by rampant non-homologous recombination between different genomes and, second, by reassortment of the variant sequences so created through homologous recombination. |
Link to this post | posted 04 Jun, 2024 17:02 | |
---|---|
|
I think Graham would probably point out that phages don't really have "lineages" in the traditional sense, which is one of the reasons we don't systematically name them——or use ICTV classifications. Phage genetic material isn't only shared vertically (between different generations), but horizontally as well. Thus, trying to shoehorn phages into classification systems designed for other types of organisms doesn't work well. From a review article Graham wrote in 2008 (this paper): "One of the most striking features of bacteriophage genomes is their apparent mosaic structure; in essence, each genome can be considered as a unique combination of modules that are exchangeable among the population. The size of the modules, their rates of exchange, and the phage genomes carrying them all vary greatly, with phages of different virion morphology, size, and host-range all participants in an orgy of recombination [36]." Hence the advice above. Just explain some version of the above to the reviewer, and let GenBank/ICTV apply whatever designations they see fit! |
Link to this post | posted 08 Mar, 2024 00:32 | |
---|---|
|
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 | |
---|---|
|
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 | |
---|---|
|
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 | |
---|---|
|
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 | |
---|---|
|
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 | |
---|---|
|
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 | |
---|---|
|
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 | |
---|---|
|
afreise Of course! Here you go: https://seaphages.org/forums/forum/222/ –Dan |
Posted in: Cluster-Specific Annotation Tips → Using This Forum