Link to this post | posted 12 Feb, 2024 19:29

debbie

Hi Elizabeth, The issue is that Cluster FC phages have just recently been found to have direct terminal repeats. Originally they were thought to be circularly permuted, which created a different sequence and end determination. What that means is that all genomes with old (incorrect) sequences at the ends) had to be reposted. That means that all phages look like draft in phamerator. It also means that the 3 that were final (Atuin, Racecar and Mimi) have to be converted to their new sequence. and revisions sent to GenBank and phamerator. That work is not quite done. But my challenge to you and your students is that, when the first 3 were done, the comparative data was sparse or non-existent. You have the opportunity to make calls with significant amounts of data and no distractions of what others have interpreted. Currently, with the data for 8 Cluster FC genomes, better information can be gathered from the comparisons - like starterator - to make really good choice about is it a gene, what is its start, and what is its function, without contradicting what others said with less than optimal (or no) comparative data available. Consider embracing this challenge because it is all good! debbie

Link to this post | posted 09 Feb, 2024 21:52

debbie

Hi Emily, Both are good questions. For the first gene, the coding potential on the GeneMark output is rather robust upstream of 37. How would you evaluate the ability of that gene to start if you are evaluating a start at base 1. What do you want to see upstream of a start to evaluate the start? How would you do that in this case? Why do you say that RBS only favors the second start? For the second gene, how is that gene going to be made? What favors the best production of that gene? Keep thinking! What did you professor have to say? best, debbie Edited 09 Feb, 2024 21:54

Link to this post | posted 09 Feb, 2024 03:37
debbie	Hi Brandon, More information is needed. What gene (please include coordinates) and genome are your inquiring about? thanks, debbie

Link to this post | posted 09 Feb, 2024 03:33
debbie	Hi ACMPhageHunters, More information is needed to help. What gene (please provide coordinates) and genome are you inquiring about? Thanks, debbie

Link to this post | posted 08 Feb, 2024 21:00
debbie	Hi Nancy, I used the posted file and was able to auto-annotate. Were other students able to annotate. sounds like something is up with the student's installation of DNA Master, or their Windows is interpreting the file as something it is not. debbie

Link to this post | posted 08 Feb, 2024 18:12
debbie	Hi Nancy, Let's see if I can help. But I need more information. Are you in DNA Master, file -> open -> FastA multiple sequence file? Is the file the .fasta file for your phagesDB phage page. Is it a text file? Can you open a different dna master file and navigate around it. Have you tried more than 1 different fasta file? debbie

Link to this post | posted 07 Feb, 2024 23:42
debbie	Adam, What do you want to call here? What is your evidence? debbie

Link to this post | posted 07 Feb, 2024 12:44
debbie	Adam, In the paper referred to the Bioinformatics Guide, the TAC 'template' is X_XX.Y_YY.Z. You have not provided enough information for me to look quickly, but check the guide to interpret the '_ 'and '.'s If your CCCTTTT lines up correctly for a -1 Frameshift, you have a canonical programmed ribosomal slippage. You also used an abbreviation 'PF' that i don't recognize. debbie

Link to this post | posted 07 Feb, 2024 03:03
debbie	Holly, Sorry for the confusion. The only program to use is DeepTMHMM. And only 1 transmembrane protein needs to be found to call a membrane protein. take care to interpret DeepTMHMM hits because some will identify signal proteins. At this time, we are not calling signal proteins. The Bioinformatics Guide is updated. debbie

Link to this post | posted 07 Feb, 2024 01:10

debbie

Hi all, If you are looking how to instal PDM utils on a M1 mac, you can follow this: On a series of MacBook Pro computers, including most recently an M1 mac, I have only ever done native installs of pdm_utils. The hardest part for me is MySQL – use an installer for 8.0.18 or later (earlier versions had funky bugs related to cascaded deletes!). Choose “Legacy Password” when prompted, and you’ll be forced to choose an 8-character or longer password (no more ‘phage’). Make sure you add mysql to the $PATH (export PATH=’/usr/local/mysql/bin:$PATH’) in your ~/.zshrc file. Other than that, if you use some flavor of conda to manage the third-party dependencies (Aragorn, trnascan-se, mmseqs2, blast) pdm_utils should be just fine. –Christian Gauthier Edited 07 Feb, 2024 01:21