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All posts created by stukey

| posted 17 Jan, 2020 17:21
Hello -

I've attached a protocol that we have worked up and use for our one-step assays. Consistent with Welkin's observation, we also find some phages work better (giving nice definitive latent period signal and obvious burst plateau) than others. But overall, we have had success in producing what I would say is good, clean data that can be interpreted and that is generally reproducible.

Joe
Posted in: Phage BiologyOne Step Growth Curve
| posted 12 May, 2018 14:59
Hi Welcome,

Thanks for your help. I see that when you validate, not all the boxes are checked as in the on-line guide. I was selecting the override box on the bottom but not all the extra boxes on top. That took care of the issue.

Joe

Posted in: DNA MasterFInal gene order renumbering issue
| posted 12 May, 2018 04:02
Hi Lee -

Thanks for pointing that out to me, but that is not the issue or appears behind the problem I am experiencing. That did set the number in the tag identifier for the first gene to 1, but the gene name remained 10 and appears as gp10 in the product box and documentation and on the genome map at the bottom. I am thinking that the first gene should have the name 1 and be shown as gp1.

Other suggestions?

Thanks again,
Joe
Posted in: DNA MasterFInal gene order renumbering issue
| posted 11 May, 2018 19:21
Hi -
Auto-annotation of one of our phage genomes (Bromden) identified a gene that wrapped around the genome and consequently had the last gene number in the original dnam5 file. After examination of the data, that gene was shortened to where the start site was now on the left end of he genome. With those changes, I can list it at the top of the features table if I sort by "start". But renumbering efforts has identified the gene as 10, not 1. And the "gp10" identifier is shown in the features and documentation notes. How can I link the sequence of genes with a proper sequence of numbers starting with 1?
Thanks,
Joe
Posted in: DNA MasterFInal gene order renumbering issue
| posted 10 May, 2018 19:24
Hi -

My question is about the request to re-BLAST all features before submitting your final DNA Master files for review. We have done that for all genes in which the start site was altered as well as for all added genes. But we did not re-BLAST all genes that were called using the original auto-annotated coordinates. Is that acceptable or do you require a complete re-BLAST be done?

Thanks,
Joe
Posted in: How to Pass Preliminary Annotation ReviewRe-BLAST final dnam5 file
| posted 19 Jan, 2018 15:40
Thanks Lee -

I didn't realize there was an "unknown" grouping and I don't think I ever scrolled to the bottom but just stopped at the K phages (we know it is a K5).

Joe
Posted in: Web PhameratorMissing 2018 draft phage genomes
| posted 19 Jan, 2018 14:58
Hi Dave -

So now I do see that our other phage isolated this year - Thyatira - is shown as being phamerated but I do not find it listed on the Phamerator webpage? Is there normally a delay between before finding it on the Phamerator site or could it be an issue of it being identified as "unclustered" at phagesdb? (We like to have our students "discover" the cluster relationships.)

Thanks.
Joe
Posted in: Web PhameratorMissing 2018 draft phage genomes
| posted 17 Jan, 2018 16:06
Thanks Dave. We will watch for that change.

Joe
Posted in: Web PhameratorMissing 2018 draft phage genomes
| posted 17 Jan, 2018 15:23
Hello -

I do not see our two new draft mycobacteriophage genomes (Bromden and Thyatira) listed on the web-Phamerator page and do not know if I am missing some step or those auto-annotated files have not yet been added to the database?

Thanks,

Joe
Posted in: Web PhameratorMissing 2018 draft phage genomes