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All posts created by asprenkle

| posted 18 May, 2021 17:13
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?!
Posted in: AnnotationList of bioinformatic software
| posted 01 Apr, 2021 20:36
Thank you Debbie!!!!!
Posted in: PECAANChoice of join in frameshift
| posted 12 Mar, 2021 07:45
Here's the other phage: Gordonia GiKK cluster CT. I'm just not getting the frameshift yet.
Posted in: PECAANChoice of join in frameshift
| posted 12 Mar, 2021 04:56
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)?
Posted in: PECAANChoice of join in frameshift
| posted 30 Nov, 2020 14:25
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 smile
Thanks for your help!
Posted in: GordoniaGordonia DNA not cutting
| posted 19 Nov, 2020 16:12
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!
Posted in: GordoniaGordonia DNA not cutting
| posted 02 Feb, 2020 13:07
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 smile
Posted in: DNA MasterTbRegions: Cannot perform this operation on a closed dataset
| posted 28 Jan, 2020 17:51
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.
Posted in: AnnotationAddressing sequencing notes
| posted 04 Oct, 2019 17:28
Thank you so much, Debbie and Welkin! I know you have so much to do. I was noticing on the phagesdb page for Hannaconda, it is not in the archives, which might lower any enthusiasm to get it out of the genome exchange and publish the sequence anyway. It was such a good exercise for us as newbies with no genome of our own though, and I'm glad we tried to tackle it.
I will keep focused on meeting the goal this second semester to get enough phage of our own to archive and sequence!
Posted in: Frameshifts and IntronsFinding introns
| posted 01 Oct, 2019 20:57
I noticed this request for help in calling introns had received no reply, and Hannaconda is still awaiting QC, whereas our other phage from the Genome exchange has received an accession number.
Is there anything I should be doing to address this?
Posted in: Frameshifts and IntronsFinding introns