SEA-PHAGES | FInal gene order renumbering issue

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 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

Link to this post \| posted 12 May, 2018 01:31
lhughes	Joe, When you validate and prepare to renumber, there are two tabs just above the options where you select your choices and rename. The second tab lets you set the interval (it can be defaulted to 10 instead of 1 sometimes). Hope that helps, Lee

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 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 12 May, 2018 13:39
welkin	Hi Joe, Did you also tell it to reassign gene names and products when you renumbered the locus tags?

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

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FInal gene order renumbering issue