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!

Link to this post | posted 18 Mar, 2021 00:17

debbie

Chris, To back up in the sequence, we run into stop codons and I don't see how to slip over them. I went back in the literature and found another paper with a list of published slippages. There is a supplemental table with lots of examples, providing a bit more confidence in the CCCAAAT sequence. (attached) I think we should call it. It is compelling that if the BK sequences slip, the BE sequences must also. Even the GeneMark shows a pattern that suggests it also overlaps/slips. I don't think I can call, it but even without HHPred data for the "T" gene, i would still suggest it is the tail assembly chaperone. Well - all of you that are looking at these phages, what do you think? debbie 112Kb

Link to this post | posted 17 Mar, 2021 21:25

debbie

Hi all, I just looked at a couple of these. In the paper referenced in the manual, the sequence XXXYYYZ is described as the canonical sequence. Right? In the 2-3 sequences that I looked at there is such a sequence CCCAAATctt (Position 22920 in Emma1919). Lee does your genomes have that sequence? Is CCCAAAT conical enough (not really found on the list)? Does HHPRED have hits for either G or T to the TAC? What other evidence is needed? I think that together we can come up with a really good answer to this (and then make changes to the other files). Let me know what you think! Lee - thanks for checking in on this one. debbie

Link to this post | posted 16 Mar, 2021 15:16
debbie	Hi Sara and students, I believe we took the function "capsid morphogenesis protein" on purpose. As I review the HHPred for this gene I am inclined to call it "capsid maturation protease and MuF-like fusion protein". What do you think? debbie

Link to this post | posted 12 Mar, 2021 15:36
debbie	Here is how I would call GiKK's frameshift. 420Kb

Link to this post | posted 12 Mar, 2021 15:21
debbie	Here is how I would call Juicer's frameshift. I use the six-frame translation in DNA Master to find the slippery sequence. I'll look at GiKK next. debbie 327Kb

Link to this post | posted 11 Mar, 2021 02:22
debbie	Follow the case study in the Bioinformatics Guide for calling the function of the genes involved in 7-Deazaguanine modifications. These are genes 1-5 in Rosebush and gene 20 in Orion. https://seaphagesbioinformatics.helpdocsonline.com/article-1596481355 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6884629/