Link to this post | posted 23 Aug, 2020 02:45
debbie	Juan, Great questions. There are a number of explanations for this. In order to best answer this, I need to know a couple of things. What school are you asking from? What phage are you talking about? Have you read the Bioinformatics Guide about auto-annotation? debbie

Link to this post | posted 19 Aug, 2020 19:56
debbie	Hi Steve, Did you restart your machine? I forwarded your message on to Steve C. debbie

Link to this post | posted 19 Aug, 2020 19:31
debbie	Hi Steve, I am having no trouble navigating Phamerator today. debbie

Link to this post | posted 17 Aug, 2020 17:37
debbie	Hi Juan, It still sounds like she is not running as administrator. When you right click on the shortcut or program name, is 'run as administrator' selected? Not sure what else it could be. debbie

Link to this post | posted 06 Aug, 2020 15:34
debbie	Steve, This has just been revised. Check out the Pre-Qo pathway case study just posted in the Bioinformatics Guide. The revised functional assignments are listed on the approved functions Google doc. August 6, 2020.

Link to this post | posted 06 Aug, 2020 15:25
debbie	This has been revised a bit, please check the approved Function Assignment list (Google doc) and the Pre Qo pathway Case Study in the Bioinformatics Guide. August 6, 2020.

Link to this post | posted 28 Jul, 2020 21:34

debbie

It seems we keep hitting the PE/PPE proteins that are only and easily found in the Mycobacteria. Rather than avoid calling them because they can be part of functions that are not yet identified, let's start adding PE/PPE family proteins to the annotations. The attached document provides useful information to what to look for when deciding if your protein of interest has all of the necessary parts. It also includes a citation for a paper for reference. A good example is Kayacho_gene 88 (Cluster B6). However, these proteins are found in lots of phage genomes, so not a cluster specific topic. debbie 7-28-20 Edited 28 Jul, 2020 21:37 115Kb

Link to this post | posted 13 Jul, 2020 21:14
debbie	Amaya, Nope. No cutoff score per se, but bigger is better. I think I only look at top hits or areas of interest. But your approach is the one that sounds reasonable. It has to make sense. debbie

Link to this post | posted 13 Jul, 2020 20:29
debbie	Claire, I sent this on to Graham. Because of the hit and significance to T4, he is incline to call this gene "Imm-like superinfection immunity protein". Please call it in your current genome. I added it to the approved functions list. Edited 15 Jul, 2020 20:32

Link to this post | posted 09 Jul, 2020 14:08
debbie	Some folks have been receiving SSL errors when trying to download GenBank files from GenBank. Jackie Washington provide a solution. The fix is to download the C++ Visual package from https://www.microsoft.com/en-us/download/details.aspx?id=5555 and restart. Shen she did that, the problem corrected. debbie Edited 09 Jul, 2020 14:10