Link to this post | posted 01 May, 2023 13:38

stukey

Deb - The question is how to get a gene Function in the Product field in the final minimal file. The process of converting some form of complete notes file into a minimal file - and showing gene Functions in the Product field - requires that a gene Function be recorded in the original Function field of a larger working file. Then after the file conversion process those Functions will be found in the Product field (and nothing will be in the Function fields) and any gene without a Function will get the Hypothetical Protein label. As Katie wrote - if you do NOT have any info in the Functions field before working through the Complete Notes file-to Minimal File conversion process, no Functions will be copied and recorded into the Product field in the minimal file, and I think all will get labeled as Hypothetical Protein. Alternatively you can simply add the correct Function to the Product field in the minimal file. Hope this is now clear. Joe

Link to this post | posted 30 Apr, 2023 16:18
stukey	Hi Katie - Before you go through the process of generating the minimal file from a larger, working file - you do need to add a gene function in the function fields for those that you have identified. Then just walk through the conversion process and all should be fine. Joe

Link to this post | posted 26 May, 2021 23:45

stukey

Hi Deb - Well, I am setting up my Complete Notes and Minimal dnam5 files. In my review of past years Complete Notes files I see that field DOES show gene product functions. Further, the images on the Bioinformatics guide, walking us though the conversion of the Complete Notes to the Minimal files also shows information in that field. But I will follow the instructions without any info in the Function field. Thanks, Joe

Link to this post | posted 26 May, 2021 19:02
stukey	Hello - I cannot find information on how to have the Function field auto-populate? I do not recall in the past needing to add that information individually for every gene with a function. But is that what needs to be done? Thank you. Joe

Link to this post | posted 10 Mar, 2021 17:09
stukey	The function queuine tRNA-ribosyltransferase - which I do not believe is any of the newly defined Pre-Qo pathway functions - is NOT on the official functions list? PenguinLover67_2 shows almost all pham members with this function? The alternative would be to label it is NKF. Joe

Link to this post | posted 10 Mar, 2021 17:09
stukey	The function queuine tRNA-ribosyltransferase - which I do not believe is any of the newly defined Pre-Qo pathway functions - is NOT on the official functions list? PenguinLover67_2 shows almost all pham members with this function? The alternative would be to label it is NKF. Joe

Link to this post | posted 11 Feb, 2021 20:00

stukey

For the BLASTp analysis done in assessing the start site, should we be reporting % SUBJECT or QUERY aligned?  DNA Master reports % SUBJECT aligned but NCBI lists % QUERY coverage.  For most cases, this will not matter as they will be at or near 100% aligned for both query and subject.  Or maybe it does not matter for this purpose, when it is used to help evaluate start site choice? I don't recall being asked this in the past or having a discussion about it. We have always used the % SUBJECT aligned value from DNA Master except when we went to NCBI or phagesdb. I cannot find a clear statement about which should be recorded.

Link to this post | posted 17 Jan, 2020 17:21

stukey

Hello - I've attached a protocol that we have worked up and use for our one-step assays. Consistent with Welkin's observation, we also find some phages work better (giving nice definitive latent period signal and obvious burst plateau) than others. But overall, we have had success in producing what I would say is good, clean data that can be interpreted and that is generally reproducible. Joe 83Kb

Link to this post | posted 12 May, 2018 14:59
stukey	Hi Welcome, Thanks for your help. I see that when you validate, not all the boxes are checked as in the on-line guide. I was selecting the override box on the bottom but not all the extra boxes on top. That took care of the issue. Joe

Link to this post | posted 12 May, 2018 04:02

stukey

Hi Lee - Thanks for pointing that out to me, but that is not the issue or appears behind the problem I am experiencing. That did set the number in the tag identifier for the first gene to 1, but the gene name remained 10 and appears as gp10 in the product box and documentation and on the genome map at the bottom. I am thinking that the first gene should have the name 1 and be shown as gp1. Other suggestions? Thanks again, Joe