Link to this post | posted 18 Sep, 2025 15:53
brueschhoff	Thanks Debbie, Very helpful. Yes, these would be phages not posted to phagesDB. I appreciate your input! Beth

Link to this post | posted 18 Sep, 2025 15:14
brueschhoff	Greetings, We were wondering, if we had a surplus number of phage that are not purified, is there a good time or way to preserve those to be processed in the future? Thank you, Beth Rueschhoff Indiana University Southeast

Link to this post | posted 28 Mar, 2024 15:58

brueschhoff

I have a question. In DoobyDoo, Feature 65 (on Phamerator), stop 45445, has some of the features of a RecA, but not all of them. Therefore, I do not believe we should call this a RecA recombinase. On this powerpoint, our cluster (DV), falls under the category of not having a RecA recombinase but calling it anyway. Does this mean that we should not call it a RecA recombinase, or that we should call it a RecA, even though it is not a true RecA recombinase? Thank you, Beth Rueschhoff Indiana University Southeast

Link to this post | posted 23 Feb, 2024 16:36
brueschhoff	Thank you so much to both of you for your help. Very interesting!

Link to this post | posted 22 Feb, 2024 15:59
brueschhoff	Sure, Sorry about that! We are annotating DoobyDoo and the phamerator feature number is 10. The stop codon is 8910.

Link to this post | posted 21 Feb, 2024 15:31

brueschhoff

Greetings, We are investigating the function of a protein with sequence: MEYMPADLARTLSAMARGTHNEICGFILDDWTLISVRNVAKLPTISFEMSMNAILGAVEMAAASGREILGTYHSHPGGSTEPSETDLHGWPRFIDGSYARYWVVTGDTVREFERTGEGSEIGFQLIHSIGIGVVVKRPEEGMDQSVPEDZ It belongs to a pham that indicates it is a metalloprotease. BLAST Hits indicate either a tail protein or a metalloprotease. If we look at HHPRED, many hits come as a metalloprotease, but without the HEXXH motif. Rather it has a JAMM/MPN Zinc Binding domain. Should we annotate this as a metalloprotease, even without the HEXXH motif? Thank you for your assistance! Beth Rueschhoff Indiana University Southeast Edited 21 Feb, 2024 15:32

Link to this post | posted 30 Mar, 2023 16:42
brueschhoff	debbie Hi Beth, Before trying anything else, have your students close the program (maybe even restart their computer) and then try again. debbie Hi Debbie, A student just tried this and got the same error. It only seems to happen on one particular feature.

Link to this post | posted 30 Mar, 2023 15:51
brueschhoff	Greetings! Sometimes, when reblasting a gene after changing the start site, students have been getting a "range check error." This sounds vaguely familiar, but I don't remember what causes this error or what to do when they get it. Any guidance is appreciated. Thank you, Beth