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 02 Feb, 2020 20:00 | |
|---|---|
|
Amy, If send me the file, I will try to fix it. debbie |
| Link to this post | posted 30 Jan, 2020 21:16 | |
|---|---|
|
|
Gene 73 of phage Krampus is best labeled as a RuvC-like resolvase. Resolvase is too general of term to use. (Determined in a conversation with G. Hatfull. |
Posted in: Cluster EF Annotation Tips → RuvC-like resolvase
| Link to this post | posted 24 Jan, 2020 20:17 | |
|---|---|
|
|
In calling the immunity repressor of a phage JF2 (gp71), we came across a peculiar finding. It seems that the immunity repressor's open reading frame has less coding potential than another open reading frame in that area. Don't be fooled! JF2's immunity repressor shows hits in HHPred to the HTH DNA binding site (N-terminus). Read Pope, et al 2011a for info about Bxz2's broken repressor. However, our gene doesn't match that N terminus either. Many (did I say many?) phages have miscalled the open reading frame as the immunity repressor. Be careful. We will fix as soon as we can. debbie |
Posted in: Cluster A Annotation Tips → Cluster A3 Immunity Repressor?
| Link to this post | posted 23 Jan, 2020 17:01 | |
|---|---|
|
|
Greg, It is 11:59am on January 23 and I was able to update with no problem. The latest update is version 5.23.3, Build2640, 22 January 2020. Are you still having problems with the update? |
Posted in: DNA Master → DNA Master Failing to Update - 01.23.2020
| Link to this post | posted 21 Jan, 2020 19:24 | |
|---|---|
|
|
Hi Ann, the answer is in Setting Preferences in the on-line Bioinformatics Guide. It is item #2 (click the box and enter "Hatfull" as the password), but check the other preferences while you are there. Thanks, debbie |
| Link to this post | posted 21 Jan, 2020 15:27 | |
|---|---|
|
|
Nancy, Hi. Your preferences are not set correctly. The NCBI servers are not available to us anymore. Check Setting Preferences in the on-line Bioinformatics Guide, #2. Click the box and the password needed is Hatfull. You may want to check all of the preference settings while you are at it. debbie |
Posted in: DNA Master → Auto-annotation fix for fall 2017 and later
| Link to this post | posted 02 Jan, 2020 21:38 | |
|---|---|
|
|
Fernando, Hi. Did you get this issue resolved. If not, please send me your file. Thanks, debbie djs@pitt.edu |
Posted in: DNA Master → TbQueries
| Link to this post | posted 14 Dec, 2019 12:57 | |
|---|---|
|
|
Susan, Hi! Start by updating your DNA Master. The current version is 5.23.3 Build 2639 from November 6, 2019. So the exact dates escape me, but the reason (I think) your version may not be working is that you do not have DNA Master pointing to the right servers. We have Glimmer and GeneMark running on our own servers. Go to 'Setting your Preferences' in the Bioinformatics Guide to check. If you still are having problems, there are more options. debbie |
Posted in: DNA Master → Auto-annotation fix for fall 2017 and later
| Link to this post | posted 03 Dec, 2019 18:25 | |
|---|---|
|
|
Steve, Excellent question, because we simply do not know. But yes, at this time, you can apply it generally! debbie |
Posted in: Choosing Start Sites → GTGA overlaps
| Link to this post | posted 03 Dec, 2019 17:52 | |
|---|---|
|
|
Dana, Thanks for the heads-up. This periodically happens due to the way GeneMark makes this available. It is corrected. Your auto-annotation should now include Glimmer and GeneMark calls. debbie |
Posted in: DNA Master → Auto-annotation fix for fall 2017 and later