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Recent Activity
All posts created by debbie
| Link to this post | posted 04 Sep, 2020 13:28 | |
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Hi all, Sorry about the timing. In talking with Dr. Lawrence, we think this is an NCBI change. I have written emails to any/all folks I can think of at NCBI who may be able to answer or direct me to who could answer the question. NLM Help Desk replied with a 2-5 response timeline. I'll keep you posted. debbie |
Posted in: DNA Master → Blast error
| Link to this post | posted 03 Sep, 2020 16:51 | |
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Steve, I just got the same error. I'll look into it from my end. debbie |
Posted in: DNA Master → Blast error
| Link to this post | posted 03 Sep, 2020 16:35 | |
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Hi Steve, You are just having a heck of time. Have you checked your DNA Master BLAST preferences? debbie |
Posted in: DNA Master → Blast error
| 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. |