Link to this post | posted 27 Apr, 2021 13:18
debbie	It could also be that a Visuals Basic package is missing https://www.microsoft.com/en-us/download/details.aspx?id=5555

Link to this post | posted 27 Apr, 2021 13:03
debbie	Hi Fernando, I think you will need to install windows drivers again. I am not sure how to do that. Can you check with your IT people? debbie

Link to this post | posted 23 Apr, 2021 00:07

debbie

Hi Kristen, This is not a quick answer. Here is where I have gotten. The top hits seem convincing that this is a UDP-galactopyranose mutase. i am hesitant to call it because that is a very specific assignment. I am worried that this gene is ~100 aa shorter than what the crystal structures of UDP-galactopyranose mutase describe, so is it missing a domain? I was not able to dig deep enough to figure out what the C-terminus domain of a UDP-galactopyranose mutase is. (I am guessing it is the missing the mutase part.) Since this is in the oxidoreductase family, I am inclined to be more generic. If you find all of the domains of a UDP-galactopyranose mutase present, then that would settle it. I just ran out of time. What do you think? debbie

Link to this post | posted 19 Apr, 2021 20:36

debbie

Hi Andy, This is a big pham of genes with no easy answers about starts. It is an easy function call, with this gene being the terminase. Starterator was not easily helpful. The conservation of the overlap may just be because that upstream gene is driving that portion of the sequence. There is no good indication for me to push to change what Glimmer and GeneMark agree on. If I recollect correctly, the N-terminus of a terminase gene is its ATPase domain. If you carve out that domain (so that your bioinformatic comparisons don't get overpowered by the rest of the protein) you may be able to align the N-terminus sequence with other ATPase domains and find an alignment that is informative. Without more data, I would stick with the start at 797. Just my two cents on the subject. debbie

Link to this post | posted 14 Apr, 2021 23:22
debbie	HI! I think this is just an artifact of programs/databases that are not quite caught up to each other. I think if you wait another day, they'll catch up to one another. debbie

Link to this post | posted 08 Apr, 2021 16:46
debbie	Hi Susan, Of the 125 A4 genomes in the database as of this writing, not counting the _Drafts, 3 are miscalled: NorthStar, LeoAvram, and Kingmustik0402. I believe I see a slippery sequence, joining at position 15418 in Lochmonster. I'll get to updating those soon. debbie

Link to this post | posted 06 Apr, 2021 00:57

debbie

Please use the RNAseq data to call genes in Cluster Q. https://pubmed.ncbi.nlm.nih.gov/23560716/ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3641587/ If you don't read this paper, it would easy to over call the genes in this cluster of genomes. In particular, there is experimental evidence for a non-coding RNA between genes 74 and 75. The paper is in direct contrast to coding potential in that region. I will revise Cluster Q genomes soon (I am writing this on April 8,2021 and it is not done yet). Please use Giles and the data in the paper as your guide as you call Cluster Q genomes. Edited 08 Apr, 2021 16:06 2.94Mb

Link to this post | posted 06 Apr, 2021 00:26

debbie

Hi Tammy, It is not a common occurrence, for sure. In this case (and I used Nellie), the coding potential for gene 30 is best, so I want to call that one for sure. However, the HHPred for 29 is compelling (I would call it a WhiB, I think.) so I really want to call it. Because their direction has them running into each other, there is really no reason that they couldn't both be transcribed. debbie Edited 06 Apr, 2021 00:29

Link to this post | posted 18 Mar, 2021 20:19
debbie	Follow the forum thread about the ribosomal slippage of the tail assembly chaperones in Cluster BK. A ribosomal slippage has been recently identified, see attachment. I used phage Comrade for this example. As of today, Comrade and its comrades will NOT reflect this call until revisions are submitted to GenBank. However, all BKs have this sequence. 209Kb

Link to this post | posted 18 Mar, 2021 17:20

debbie

So to simplify/clarify, we will call the tail assembly chaperone and the above described slippage in the BKs. (I will get the genomes in GenBank updated soon.) We will call the BE genes as tail assembly chaperones, but will not include the slippage because it is not clear how to record that. Chris and Lee - Thank you for your input on this! A lovely demonstration on how the alliance works. Joyce, no worries about your poster. Change as you see fit. Does your title still fit? Because of the early dates for the symposium, we are all works in progress and this is such a nice story. Please mention how the forum informed. Very nice!