Link to this post | posted 14 Dec, 2020 22:08

Juan.MartinezV

Our group are about to finish the annotation of two phages (Parliament and Illumine) and we are checking for all the details prior the submit but I have a question regarding two points: 1) I use other phage annotations (Tubs or OkCentral2016) to check that I have not missed anything but in the complete notes (.dnam5) these phages are already assigned with the gene protein number (gp12, 48 and so on). All I've have seen in the annotation guide is that we should rename the product field with hypotetical proteins when we don't know the fuction (throughthe renumbing method) but then, this label of gpXY is done by us or is it assigned when is already on GenBank? 2) Kind of the same question regarding the hypotetical proteins. I am generating the minimal file and what I suposed to have is CDS 379 - 1161 /gene="1" /product="Hypothetical Protein" /locus tag="SEA_MYPHAGE_1" but I am having CDS 379 - 1161 /gene="1" /function: terminase (as example) /product="Hypothetical Protein" /locus tag="SEA_MYPHAGE_1" If I am not wrong, I just need to have a hypotetical protein in product when the fuction is unknow and a function for that gene (when we know it) but not both right? I appreciatethe time to answer Thanks! JM

Link to this post | posted 23 Aug, 2020 02:54

Juan.MartinezV

Hello Debbie We are from Mexico (Universidad Autonoma de Nuevo Leon) and we are talking about Puknovik (https://phagesdb.org/phages/Pukovnik/). I read the Bioinformatics Guide and says a lot about delete or add genes depending on the information from the other tools. For what I remember, the phagesdb was the references but I wanted to be sure about this. If there is some article that I should follow on the guide, I'll be more than happy to check it! Thanks JM

Link to this post | posted 22 Aug, 2020 17:29

Juan.MartinezV

Hello, Some of my new classmates and I are annotating a phage from last semester (to practice). After running the auto annotation we have 93 genes on DNA MASTER and according to PhagesDB there are 89, the coordinates from these genes are different on both sites. One of the "quality" steps to have in mind when we are about to finish the annotation is "to have" the same number of genes on DNA MASTER and PhageDB, so my questions are: 1) Is PhageDB the ultimate reference to know how many genes there has to be in a genome? 2) Do the coordinates have to be the same on DNA MASTER and PhagesDB? Thanks! JM Edited 22 Aug, 2020 17:30

Link to this post | posted 21 Aug, 2020 01:50
Juan.MartinezV	Hello, I have the same problem, since last week, I have been not able to access Phamerator, I already did the basic troubleshooting (clean, update, check). I use a dual system (Windows/Linux) and it is not working in this or other computer nearby me, but it seems that it is working for other people and I wonder why? Greetings. JM

Link to this post | posted 17 Aug, 2020 17:46
Juan.MartinezV	Hi Debbie, Yes, exactly as you said, we ran the program as administrator but it is still showing the same message. We already updated DNA MASTER, uninstall and install again in a different location, followed by the guide (https://phagesdb.org/media/docs/DNAMasterInstallationGuide.pdf), but I'm running out of ideas haha JM

Link to this post | posted 17 Aug, 2020 17:22

Juan.MartinezV

Hello everyone, One of my classmates is having problems with DNA MASTER. We followed the recommendation where she did not install directly in the C://Programs, instead she chose the desktop, but after she imported the sequence to run an auto-annotation, an error message displays saying "Can't create file": Access Denied. Any recommendation? Thanks! PD: She's running with admi privileges JM Edited 17 Aug, 2020 17:25 119Kb

Link to this post | posted 18 Jun, 2020 22:23
Juan.MartinezV	Hello, considering that I want to compare 2 o 3 phage genomes that are not on phamerator web, what it would be the best route to compare these genomes? I recently changed OS system from Windows to Ubuntu, but I did not find anything related to install or try phamerator in Ubuntu/Linux JM

Link to this post | posted 23 Apr, 2019 22:13

Juan.MartinezV

I have two questions about the RBS data that we are going to fill in our annotation, the guide says that we must write [NA/Scoring Matrix, spacing matrix, Z score, Final score, yes/no](1), and the way we used to calculate the RBS (2). 1) Is necessary all that information, because at the time to write it could be a little bit confusing and also, what does yes/no are the for? 2) I thought that we were going to be able to find this information in DNA Master –> ORG –> RBS I am working with phage Tubs. Thanks! JM