Link to this post | posted 12 May, 2018 01:31
lhughes	Joe, When you validate and prepare to renumber, there are two tabs just above the options where you select your choices and rename. The second tab lets you set the interval (it can be defaulted to 10 instead of 1 sometimes). Hope that helps, Lee

Link to this post | posted 17 Apr, 2018 20:09
lhughes	Welkin Pope Crosby is for Sidney, no? Wasn't sure what you were asking until I googled it Thanks on the name edit to "DNA binding, HU-like domain" Edited 17 Apr, 2018 20:41

Link to this post | posted 17 Apr, 2018 18:40

lhughes

I am looking at Cluster BH phages and have found a product that doesn't seem to fit the existing types of DNA binding proteins already on the official list. The HHPRED results for Crosby_9225-8866 gene product are attached. Hits are at 99% probability and e-values of 10^-21 and coverage over most of the query. There are a number of hits called DNA-binding HU or Histone-like. A paper that talks about a possible role of one of these hits in DNA bending is http://emboj.embopress.org/content/22/14/3749 . On PECAAN, the Conserved Domain hits are also to this HU-like domain. Currently, all the members of the Pham are found in Cluster BH phages only. I suggest that we add a new type of DNA binding function "DNA binding protein, HU-like" Lee 83Kb

Link to this post | posted 17 Apr, 2018 18:26
lhughes	Thanks, Eric. This Pham appears to only have members from Cluster BH, so nothing out there before appears to have this particular match. I'll write it up and make a new post under the "Request a New Function" topic. Lee

Link to this post | posted 09 Apr, 2018 20:20
lhughes	I'll jump in and Pitt can tell us if this answer isnt' correct: I consider that message not an "error message" but instead a notification. DNA Master is notifying me that these two genes share a start. In the case of a frameshift, that is what I wanted so everything is fine. In other cases, this helps me to catch duplicate genes that were accidentally left in the feature list. Lee

Link to this post | posted 02 Apr, 2018 15:35
lhughes	Like in Cluster A phages, the DNA primase of many cluster BD phages is split into two overlapping reading frames. The upstream portion of the gene is frequently missed by Glimmer and Genemark. We are not sure what happens within the cell during the infection to generate the correct full length primase, so for now, we add both parts to the annotations with a large overlap.

Link to this post | posted 30 Mar, 2018 14:55

lhughes

I am looking at Cluster BH phages and have found a product that doesn't seem to fit the existing types of DNA binding proteins already on the official list (at least as far as I can see). The HHPRED results for Crosby_9225-8866 gene product are attached. Hits are at 99% probability and e-values of 10^-21 and coverage over most of the query. There are a number of hits called DNA-binding HU or Histone-like. A paper that talks about a possible role of one of these hits in DNA bending is http://emboj.embopress.org/content/22/14/3749 Please help me determine if this fits an existing category or needs to be explored more for a new function. Thanks! Lee 83Kb

Link to this post | posted 02 Mar, 2018 15:17

lhughes

Steven Caruso We have looked very closely on all our Strep. phages (BG, BH, BI, etc.), and couldn't find them. I'm glad it's not just us. But we'll keep looking! Steve - Be careful not to confuse "B" cluster with the double letter "BB,BG" etc. clusters. Welkin is talking about just the Cluster B phages in this topic. Several of the Streptomyces-associated clusters have the Tail assembly chaperone frameshift (including Clusters BC, BD, and BL). Lee

Link to this post | posted 23 Jan, 2018 19:18
lhughes	If you click the white space next to the cluster designation (not the box or the cluster letters), it will open up and show you all the members of that cluster. You can then check on just the boxes of the ones you want to view. You can do the same thing with other clusters to pick additional phages from other clusters to map. Lee

Link to this post | posted 19 Jan, 2018 15:07

lhughes

Joseph Stukey Hi Dave - So now I do see that our other phage isolated this year - Thyatira - is shown as being phamerated but I do not find it listed on the Phamerator webpage? Is there normally a delay between before finding it on the Phamerator site or could it be an issue of it being identified as "unclustered" at phagesdb? (We like to have our students "discover" the cluster relationships.) Thanks. Joe Joe, I was just looking and see it under the "UKN" designation on the list on the web Phamerator. Lee