Link to this post | posted 09 Feb, 2021 16:10

kmaclea

Thank you for that, Vic! I've got my fingers crossed for the enriched right now, we should know how our first run went soon. I had avoided getting soil before the frost since the guide had suggested fresh was best. I did get a good direct isolation from a place we isolated from last year so I do think your words about going back to the same spot could be prescient. Regardless–thank you! Hopefully some good success soon. Thanks! Kyle – Kyle MacLea Associate Professor, University of New Hampshire at Manchester kyle.maclea@unh.edu +1 603-641-4129

Link to this post | posted 05 Feb, 2021 18:27
kmaclea	Added: We started with A. globiformis and had no luck, and tried again with M. foliorum and also had no luck. – Kyle MacLea Associate Professor, University of New Hampshire at Manchester kyle.maclea@unh.edu +1 603-641-4129

Link to this post | posted 05 Feb, 2021 18:26

kmaclea

Dear Colleagues We are running phage discovery in the winter for the first time. Our first go-round we have a lot of success with direct isolations out of the box. This might have been an outlier leading us astray, but over the last couple of weeks we only had one successful run with direct isolation. We have started enriched isolation but still wondering if we can do better with our direct isolation or if winter in New Hampshire is just going to be more challenging. Anyone have thoughts? Kyle – Kyle MacLea Associate Professor, University of New Hampshire at Manchester kyle.maclea@unh.edu +1 603-641-4129

Link to this post | posted 11 Nov, 2020 17:08
kmaclea	Dear Dan That is exactly what I needed to get started on this. I really appreciate all the links and tips. I will plan to try this out and then of course bounce this off of you for corrections and helpful advice–BIG help to me, thank you. All best, Kyle – Kyle MacLea Associate Professor, University of New Hampshire at Manchester kyle.maclea@unh.edu +1 603-641-4129

Link to this post | posted 11 Nov, 2020 17:08
kmaclea	Dear Dan That is exactly what I needed to get started on this. I really appreciate all the links and tips. I will plan to try this out and then of course bounce this off of you for corrections and helpful advice–BIG help to me, thank you. All best, Kyle – Kyle MacLea Associate Professor, University of New Hampshire at Manchester kyle.maclea@unh.edu +1 603-641-4129

Link to this post | posted 11 Nov, 2020 05:16

kmaclea

So, I have a fair bit of experience assembling bacterial genomes on a basic level. Let's say I want to do my own phage genome sequencing, and then assembly. Obviously, to get the best quality control and the benefit of all your experience, getting your eyeballs on the assembly is probably critical. But is there a process written anywhere with the typical Newbler or other parameters you use for assembly? How much is customized on each assembly run? Is there a pathway where we could sequence and assemble on our own but then ask for your review of our assembly and if you concur with our assembly? Or would that be totally on our own? Thank you as always! Kyle – Kyle MacLea Associate Professor, University of New Hampshire at Manchester kyle.maclea@unh.edu +1 603-641-4129

Link to this post | posted 04 Sep, 2020 20:04
kmaclea	Thank you, Debbie. I've also noticed they are extremely variable with activation times. It's odd because they create the number so you'd think putting it up would be easy once you have that, but I guess not! Thanks! Kyle – Kyle MacLea Associate Professor, University of New Hampshire at Manchester kyle.maclea@unh.edu +1 603-641-4129

Link to this post | posted 04 Sep, 2020 19:25

kmaclea

So I was just browsing and saw our first phage, Yavru, is reported as "In Genbank" and has an accession number. But the number leads nowhere and NCBI these days is horrible to browse and find anything in Genbank (at least in my hands). MT889364: http://www.ncbi.nlm.nih.gov/nuccore/MT889364 Any tips to find the sequence? Want to show the students their names in lights! Kyle= – Kyle MacLea Associate Professor, University of New Hampshire at Manchester kyle.maclea@unh.edu +1 603-641-4129

Link to this post | posted 07 Apr, 2020 02:00
kmaclea	Fantastic! Thank you, Dan! Kyle – Kyle MacLea Associate Professor, University of New Hampshire at Manchester kyle.maclea@unh.edu +1 603-641-4129

Link to this post | posted 04 Apr, 2020 20:31

kmaclea

debbie 2. What are the end types of your genome? Can you figure out your question about the last 2 genomes once you know that? You will want to be very careful how you annotate both ends of your genome. I missed a little discussion at the workshop about End types. Can you point to some good reading on this? Thank you! Kyle – Kyle MacLea Associate Professor, University of New Hampshire at Manchester kyle.maclea@unh.edu +1 603-641-4129