Link to this post | posted 28 Jun, 2019 15:51
welkin	I've heard back from Bjorn CAnback— he is aware that the server is down and is working to bring it back online.

Link to this post | posted 26 Jun, 2019 18:55
welkin	REgarding the HNH and DNA methylase overlap– we have some wet bench evidence that out-of-frame HNHs are made when found within the context of overlapping a DNA methylase or DNA polymerase gene. So in these instances, it is OK to call both genes, even with the large overlap– as long as you are confident that both are intact and functional.

Link to this post | posted 26 Jun, 2019 18:52

welkin

From Amy Sprenkle: "We from cohort 11 adopted a Cluster J phage in the spring of 2019 to make sure we really got trained in all of the bioinformatics tools available. Hannaconda did not disappoint. I relied heavily on the Pope J Cluster paper for guidance, and worked on the TAC frameshift successfully from the excellent bioinformatics guide and help from Welkin. We used PECAAN and had two tRNAs called, and I learned at the symposium that the web-based aragorn would call introns as well. I failed to throughly explore this tool before submitting the genome, so I will continue to work on that. I message in this string because when searching for J cluster and introns, this is what pops up. It is not at all clear to me how one uses phamerator to see the introns, because they are not described in phamerator the way they are in the paper. Also, some of the J phage from the paper have an intron and others do not. Those that do are not consistent with regard to their association with HNH endonucleases. Any help with better calling of an intron would be appreciated."

Link to this post | posted 26 Jun, 2019 16:56
welkin	copied over from Cluster J annotation tips. Intron question has been moved to "Frameshifts and Introns" Edited 26 Jun, 2019 18:53

Link to this post | posted 25 Jun, 2019 16:15
welkin	It also doesn't load for me. Time to send an email ???

Link to this post | posted 05 Jun, 2019 14:31
welkin	yep– absolutely I would delete it. Good instincts! Thanks for asking!

Link to this post | posted 03 Jun, 2019 18:46
welkin	OK, I completely agree with deleting gene 35 shown in your screenshot from your annotation; I am hoping that Snazzy is the middle genome you are showing here. Could you upload similar pictures of the other site you are concerned about?

Link to this post | posted 03 Jun, 2019 17:42
welkin	Here is an example of where the overlapping primase gene should be added to a cluster A annotation. Power point slide by Chris Brey. 276Kb

Link to this post | posted 23 May, 2019 20:47

welkin

But the back end of Pol I is where the polymerase part is. right? So I see a pretty good full length alignment ( I reran to see all the matches) starting part of the way through Pol I and running through to the end. IF you look farther down the HHPred matches the first domain of the phage protein aligns to solo 3'-5' exos, which is the middle of Pol I. and the back half of ours is a polymerase domain. So the missing bit in the phage gene is the 5'-3'exo, that is at the beginning of E coli pol I.

Link to this post | posted 23 May, 2019 17:54
welkin	Hi Sally– In the second picture you show, the protein is aligning to the crystal structure of the Klenow fragament; which according to the first picture you show, includes the polymerase and the 3'-5' exo domains, but not the 5'-3' exo domain. Correct?