Link to this post | posted 27 Feb, 2023 18:29
asprenkle	Microbacterium phage BabyDaisy (EB) pham 67090 called both portal protein and MuF-like fusion protein as recently as 2021 see attached screenshot. Official function list says do not call Mu, just portal. Please advise. Edited 27 Feb, 2023 18:29 70Kb

Link to this post | posted 27 Feb, 2023 18:28
asprenkle	Microbacterium phage BabyDaisy (EB) pham 67090 called both portal protein and MuF-like fusion protein as recently as 2021 see attached screenshot. Official function list says do not call Mu, just portal. Please advise.

Link to this post | posted 18 May, 2021 17:13

asprenkle

This is still a very useful list, thanks! The reason I was scanning it was to look for some off, off site software that I came across when I was looking for a way to count cells in an a micrograph. This freeware came across my browser: https://www.dnabaser.com/contact/index.html They are out of Romania and also have assembly software that I thought someone may have seen. I'm wary of downloading any software from Eastern Europe, thoughts?!

Link to this post | posted 01 Apr, 2021 20:36
asprenkle	Thank you Debbie!!!!!

Link to this post | posted 12 Mar, 2021 07:45
asprenkle	Here's the other phage: Gordonia GiKK cluster CT. I'm just not getting the frameshift yet. 649Kb

Link to this post | posted 12 Mar, 2021 04:56

asprenkle

I am trying to do the programmed translational frameshift in a Microbacterium EA6 phage, Juicer. I attended the 2020 Hackathon and saw Claire's excellent post in this forum about doing it in PECAAN, but I think I have two possible candidates for the join and would appreciate suggestions. I have screengrabs of the two regions along with the GM output in the attached document. I'm thinking the join should be 10397 OR 10367. Both are -1 and have listed slippery sequences around a Glycine. Should I be trying to BLAST the protein sequence with a related phage (Chepli)? 921Kb

Link to this post | posted 30 Nov, 2020 14:25
asprenkle	I was finally able to get cutting, and with NspI but not HindIII. I did not use other enzymes after Dan suggested he only needed to see UC DNA, so I was being frugal with enzymes and gel lanes. I had omitted the 65C incubation after DNA isolation. That is clearly a necessary step Thanks for your help!

Link to this post | posted 19 Nov, 2020 16:12
asprenkle	Anyone have any trouble getting a good RE digest of Gordonia DNA? I've got good DNA from M. foliorum, and we're trying Gordonia rubripertincta for the first time this year. I've noticed it's a bit waxier than M. foliorum. I'm getting OK DNA concentrations with a new Wizard kit, but my Mf DNA cuts where my Gr does not. Any tips/tricks I'm missing? Thanks!

Link to this post | posted 02 Feb, 2020 13:07

asprenkle

After BLASTing all genes, saving the file with a new name, and re-opening, I get all blanks and this message: SQL:Cannot perform operations on a closed dataset I tried the unpack/pack from the link above, and the file size is now larger, but I still see nothing in any tab but the sequence. This only happened in one of our two phages this semester. I will repeat by comparing the successful one with the corrupted one and keep trying, but any additional guidance would be appreciated. I am doing this on my home computer that is hardwired, since I tend to run the NCBI blasts overnight. However, it also belongs to my software engineer partner, so all bets are off, and if I ask him for help, I'm in for a long, long day of frustration

Link to this post | posted 28 Jan, 2020 17:51
asprenkle	M. foliorum phage Jerky has this sequencing note: The sequencing reads indicate that in ~40% of the phage population from which DNA was extracted, there is a deletion of 45 bp from 13248 to 13292, inclusive. Should this be addressed in the annotation? We are just getting started, so we don't know yet if there is something interesting there.