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Recent Activity
All posts created by stukey
| Link to this post | posted 11 May, 2018 19:21 | |
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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
| Link to this post | posted 10 May, 2018 19:24 | |
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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 | |
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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
| Link to this post | posted 19 Jan, 2018 14:58 | |
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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
| Link to this post | posted 17 Jan, 2018 16:06 | |
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Thanks Dave. We will watch for that change. Joe |
Posted in: Web Phamerator → Missing 2018 draft phage genomes
| Link to this post | posted 17 Jan, 2018 15:23 | |
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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