Link to this post | posted 24 Jan, 2020 20:17

debbie

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

Link to this post | posted 23 Jan, 2020 17:01
debbie	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?

Link to this post | posted 21 Jan, 2020 19:24
debbie	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
debbie	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

Link to this post | posted 02 Jan, 2020 21:38
debbie	Fernando, Hi. Did you get this issue resolved. If not, please send me your file. Thanks, debbie djs@pitt.edu

Link to this post | posted 14 Dec, 2019 12:57

debbie

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

Link to this post | posted 03 Dec, 2019 18:25
debbie	Steve, Excellent question, because we simply do not know. But yes, at this time, you can apply it generally! debbie

Link to this post | posted 03 Dec, 2019 17:52
debbie	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

Link to this post | posted 22 Nov, 2019 17:16
debbie	Here is what I know so far. A slippery sequence could not be found in the original EA1 and EA2 annotations. We have looked at EA1 - EA8 annotations so far. Slippery sequences have been annotated in Subclusters EA3,EA4,EA5,and EA6, not in Subclusters EA1, EA2, EA7, and EA8. So if you can find a canonical sequence for the slippage, i would recommend calling it. if you can't, then don't. 212Kb

Link to this post | posted 17 Nov, 2019 18:37

debbie

There are 2 overlapping open reading frames that can show up in your auto-annotations that are ~ the same size somewhere in the vicinity of bp 22,200. One is a HHpred hit to a helicase (difficult to differentiate further, for now). The other does not have significant hits to anything. Be careful to pick the right one. (There are incorrect calls in the database - to be correct.) An example of a good call is Wayne gp29. 11-17-19 debbie