Link to this post | posted 12 May, 2018 14:59
stukey	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

Link to this post | posted 12 May, 2018 04:02

stukey

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

Link to this post | posted 11 May, 2018 19:21

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

Link to this post | posted 10 May, 2018 19:24
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

Link to this post | posted 19 Jan, 2018 15:40
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

Link to this post | posted 19 Jan, 2018 14:58
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

Link to this post | posted 17 Jan, 2018 16:06
stukey	Thanks Dave. We will watch for that change. Joe

Link to this post | posted 17 Jan, 2018 15:23
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