Welcome to the forums at seaphages.org. Please feel free to ask any questions related to the SEA-PHAGES program. Any logged-in user may post new topics and reply to existing topics. If you'd like to see a new forum created, please contact us using our form or email us at info@seaphages.org.
Recent Activity
JustinA posted in Plaques appear on spot test, don't appear in titer
Viknesh Sivanathan posted in Plaques appear on spot test, don't appear in titer
JustinA posted in Plaques appear on spot test, don't appear in titer
Viknesh Sivanathan posted in Plaques appear on spot test, don't appear in titer
RyanWheeler posted in Plaques appear on spot test, don't appear in titer
All posts created by debbie
Link to this post | posted 09 Sep, 2020 01:45 | |
---|---|
|
Steve, Check the build, I think that he has not updated DNA Master. debbie |
Link to this post | posted 08 Sep, 2020 19:52 | |
---|---|
|
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 | |
---|---|
|
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 | |
---|---|
|
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 | |
---|---|
|
No worries. Par for the course. |
Link to this post | posted 04 Sep, 2020 13:28 | |
---|---|
|
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 | |
---|---|
|
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 | |
---|---|
|
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 | |
---|---|
|
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 | |
---|---|
|
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. |