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
All posts created by debbie
| Link to this post | posted 14 Oct, 2021 20:12 | |
|---|---|
|
Amanda, HI! Sorry for the delay in my response too! Claire and the PECAAN folks purposely made the PECAAN output meet the QC requirements for each gene of an annotation. So i don't think that any modifications are needed from the PECAAN output. Use the cover sheet to describe what you have done and all should work out. debbie |
Posted in: Notes and Final Files → Question about notes template
| Link to this post | posted 17 Sep, 2021 16:24 | |
|---|---|
|
|
Hi all, My last posts were misguided. It was the license problem. GeneMark is back on line! debbie |
Posted in: DNA Master → Auto-annotation fix for fall 2017 and later
| Link to this post | posted 16 Sep, 2021 21:12 | |
|---|---|
|
|
I just talked to Christian and he suggested the simplest explanation is the Preference Settings in the Secure Connections panel are not set properly. See the attached picture for what they should look like. Going forward, would you let me know if you still have problems what DNA master build number you are using. (The latest build that i have is 2704.) Thanks! |
164KbPosted in: DNA Master → Auto-annotation fix for fall 2017 and later
| Link to this post | posted 16 Sep, 2021 21:04 | |
|---|---|
|
|
Good info. I have no idea if this will have any impact. The latest 'fix' is about active and passive FTP. Make sure that in your preferences -> Internet setting ->Home Site that you match the setting that I have. (This is the only preference i have modified lately.) And as another data point, I auto-annotated a new to me genome this morning and DID get GeneMark data in my auto-annotation. debbie |
143KbPosted in: DNA Master → Auto-annotation fix for fall 2017 and later
| Link to this post | posted 16 Sep, 2021 00:25 | |
|---|---|
|
|
Kathleen, Here is the next thing that I would like you to check/try. Check out your auto-annotation choices. Do you have both analyses checked as int he attached photo? Thanks, debbie |
113KbPosted in: DNA Master → Auto-annotation fix for fall 2017 and later
| Link to this post | posted 15 Sep, 2021 21:34 | |
|---|---|
|
|
Hi Kathleen, Would you try again? I just auto-annotated a genome and got GeneMark results. The license to use GeneMark's server seems to be dependent on use, so it is not easy to predict when we have to update it. It could have just been updated after you auto-annotated. If that is true then you will get GeneMark results when you repeat. If you don't get GeneMark results when you repeat, I am not sure what the problem is and will investigate further. Keep me posted, debbie |
Posted in: DNA Master → Auto-annotation fix for fall 2017 and later
| Link to this post | posted 31 Aug, 2021 02:11 | |
|---|---|
|
|
Hi all. Kristen is correct. We are aware of this issue and are working on it. debbie |
Posted in: DNA Master → DNA Master Issue
| Link to this post | posted 20 Aug, 2021 15:44 | |
|---|---|
|
|
Yes. I think so. |
Posted in: DNA Master → DNA Master Issue
| Link to this post | posted 20 Aug, 2021 14:56 | |
|---|---|
|
|
Hi! I think that this is the issue: If the 'Use PBI server…" is not on your screen, you still need to update DNA Master to continue. Be sure to update as an administer. debbie |
Posted in: DNA Master → DNA Master Issue
| Link to this post | posted 04 Aug, 2021 19:04 | |
|---|---|
|
|
In addition to the terminase, large subunit in cluster J phages, they contain another gene (gp3 in Omega) that hits the N-terminus of terminase. Please refer to the Cluster J paper for further explanation of this gene call. https://pubmed.ncbi.nlm.nih.gov/23874930/ |
Posted in: Cluster J Annotation Tips → Terminase? gene