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All posts created by stukey

| posted 11 May, 2018 19:21
stukey avatar
stukey
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 Master → FInal gene order renumbering issue
| posted 10 May, 2018 19:24
stukey avatar
stukey
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 Review → Re-BLAST final dnam5 file
| posted 19 Jan, 2018 15:40
stukey avatar
stukey
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 Phamerator → Missing 2018 draft phage genomes
| posted 19 Jan, 2018 14:58
stukey avatar
stukey
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 Phamerator → Missing 2018 draft phage genomes
| posted 17 Jan, 2018 16:06
stukey avatar
stukey
Thanks Dave. We will watch for that change.

Joe
Posted in: Web Phamerator → Missing 2018 draft phage genomes
| posted 17 Jan, 2018 15:23
stukey avatar
stukey
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 Phamerator → Missing 2018 draft phage genomes