Link to this post | posted 08 Sep, 2020 19:52

debbie

Jasmin, HI. There are 2 common errors that can cause this. One is that our permission to use the Glimmer server ran out and needs to be updated. I have ruled that out because I was able to auto-annotate and obtain Glimmer results. The second reason is usually that the settings are incorrect in Preferences. Have them check # 2 at this page of the guide. The unlock code is Hatfull; there is no password. https://seaphagesbioinformatics.helpdocsonline.com/article-66

Link to this post | posted 05 Sep, 2020 13:16
debbie	An update to DNA Master has been posted. Blast will not work unless you update. The latest version is Version 5.23.3 Build 2657 4Sep2020

Link to this post | posted 04 Sep, 2020 19:46
debbie	Kyle, It is up to GenBank. They promise an accession number in 3 days when a genome is submitted. Then they have to process it. That time is unpredictable. My last submissions took ~ month. debbie

Link to this post | posted 04 Sep, 2020 14:15
debbie	No worries. Par for the course.

Link to this post | posted 04 Sep, 2020 13:28
debbie	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

Link to this post | posted 03 Sep, 2020 16:51
debbie	Steve, I just got the same error. I'll look into it from my end. debbie

Link to this post | posted 03 Sep, 2020 16:35
debbie	Hi Steve, You are just having a heck of time. Have you checked your DNA Master BLAST preferences? debbie

Link to this post | posted 27 Aug, 2020 01:07
debbie	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

Link to this post | posted 23 Aug, 2020 03:17

debbie

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. Edited 24 Aug, 2020 16:05

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