Link to this post | posted 25 Jun, 2018 17:35

lhughes

I get the following error from the final Phamerator file check after submission: "SparkleGoddess failed to be imported into Phamerator for the following reason(s): -tRNA at 77662 doesn't appear to have the correct terminal nucleotide" The tRNA is called by Aragorn, but not by tRNA-ScanSE. The acceptor stem does seem to be odd (one mismatch but seven matches) and of course the error above about terminal nucleotide (you can find this genome in PECAAN, but screenshot of the Aragorn output in PECAAN attached). Should this call be deleted? A similar genome, Comrade, has the same error (tRNA at 77362 in that genome). Let me know your thoughts and then I will make corrections to resubmit the genomes to PhagesDB. Lee 79Kb

Link to this post | posted 22 Jun, 2018 18:04
lhughes	Ok - thanks. I'm glad it wasn't just me. I'll make the updates manually in the files that I am submitting. Lee

Link to this post | posted 22 Jun, 2018 03:57

lhughes

I am working on 4 Cluster BK1 genomes which all have lots of tRNAs. When I reached my final review of the genomes and comparisons of their labeled functions, including tRNA, I was surprised to find that the tRNA notes were not matching the tRNA output from Aragorn/tRNAScan. Basically, what I think is happening is that the exported notes are showing the Codon sequence, not the Anticodon sequence. For example, in Annadreamy, the first tRNA (4218-4145 Reverse) shows the anticodon as GGT when you look at the Aragorn/tRNA scan information, but the output from PECAAN gives it as ACC. The reason I noticed it originally was because I had downloaded another BK1, Blueeyedbeauty, sometime last year and it had GGT in the output (but if I re-download now it gives me ACC). Please help me figure this out. These genomes each have over 35 tRNAs in them so I need to make sure I'm getting them in the correct format (and hopefully this is not an issue for others who've done tRNA's recently). Thanks, Lee

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