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Recent Activity
All posts created by debbie
Link to this post | posted 27 Aug, 2020 01:07 | |
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Hi Sean, Yes DNA Master can handle most anything from NCBI. The version we have is for prokaryotes. So I believe there are better programs for hanfle introns and exons and such. debbie |
Posted in: DNA Master → Using DNA Master beyond phages
Link to this post | posted 23 Aug, 2020 03:17 | |
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Juan, Mycobacterium phage Pukovnik was found in 2005 and is in GenBank and part of numerous publications, including this one. https://pubmed.ncbi.nlm.nih.gov/24112940/ It is no longer in its draft form but has been hand curated and modified. In addition, there is experimental data to support some of the gene calls. Because Pukovnik is in GenBank, PhagesDB genes reflect that record. A DNA Master auto-annotation represents the Draft version of a file that is then curated by annotators like you. PhagesDB will report the data that that should be most complete, so if it is in GenBank. However, if it is a new genome, phageDB will post the draft information. In addition, if the data is in draft form, Phages DB (and Phamerator) may not match your DNA Master auto-annotation because of the way that the data is generated. |
Link to this post | posted 23 Aug, 2020 02:45 | |
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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 | |
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Hi Steve, Did you restart your machine? I forwarded your message on to Steve C. debbie |
Posted in: Phamerator → Phamerator down?
Link to this post | posted 19 Aug, 2020 19:31 | |
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Hi Steve, I am having no trouble navigating Phamerator today. debbie |
Posted in: Phamerator → Phamerator down?
Link to this post | posted 17 Aug, 2020 17:37 | |
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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 |
Posted in: DNA Master → Can't create a file after Auto-Annotation
Link to this post | posted 06 Aug, 2020 15:34 | |
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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 | |
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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. |
Posted in: Cluster B Annotation Tips → GTP cyclohydrolase I
Link to this post | posted 28 Jul, 2020 21:34 | |
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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 |
Posted in: Annotation → PE/PPE proteins
Link to this post | posted 13 Jul, 2020 21:14 | |
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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 |
Posted in: Phage Biology → Promoter prediction