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All posts created by stpage

| posted 19 Feb, 2021 17:30
Is the DNA master server ftp://cobamide2.bio.pitt.edu/DNAMas/dna%20master.exe having trouble this week or is it us?

Shallee
Posted in: DNA MasterDNA master server down?
| posted 09 Mar, 2020 20:24
Pham95856 still has a range of functions listed: Within that pham, there are functional annotations for RNAseE, sigma factor, DNase, endoribonuclease and just helix-turn-helix DNA binding domain protein. I know some B cluster in that pham were changed from RNAseE to helix-turn-helix DNA binding domain protein. Is that the best choice for our DR cluster.
Posted in: Functional Annotationribonuclease function
| posted 03 Mar, 2020 20:43
Yeah, that location in Mariokart is just AGGGCCG….
Yago84 did not call the frameshift but there is a aagggcct
So maybe I should just follow that.
Posted in: Cluster DR Annotation TipsTail Assembly Chaperone
| posted 03 Mar, 2020 17:15
Thanks again, Erin. It makes more sense looking at the GenBank entry rather than Phamerator. I don't have that many Gs, but I'll try a mockup of the frameshift and see how it looks in Mariokart.
Posted in: Cluster DR Annotation TipsTail Assembly Chaperone
| posted 02 Mar, 2020 01:48
Not annotating frameshift in absence of wet bench evidence, GC-rich region but not obvious slippery sequence. Some in cluster have two tail assembly chaperone back to back in same frame (Sour, NHagos), most overlapping in separate frames (Cloverminnie, Mariokart).
Posted in: Cluster DR Annotation TipsTail Assembly Chaperone
| posted 23 May, 2019 22:05
The CP is almost nonexistent, and it is less than 2/3 the length of the BE ones, though. Blasting the first primase of a BD (Alvy) vs the putative first primase of the BE is 30%coverage 35% aa alignment, which is intriguing not very convincing…

THe BLAST alignment for that ORF is about the same with Karimac, your BD phage, too…
Edited 23 May, 2019 22:11
Posted in: Cluster BD Annotation TipsDNA Primase
| posted 23 May, 2019 01:38
What about BE phages? They have a similar pattern. Several BE have a gene upstream of primase that overlaps with only fair coding potential (e.g., Karimac) that Glimmer and GM don't like. Can we call that DNA primase, too?
Posted in: Cluster BD Annotation TipsDNA Primase
| posted 11 Apr, 2017 18:14
The last couple of days, I can't open the Lawrence Lab web page to download DNA master…
Posted in: DNA MasterDNA Master failed update
| posted 06 Oct, 2016 17:09
Thanks, Dan. (And, the direct link to SEAVM helped a lot too)
Posted in: SEA-PHAGES Virtual MachineWINE
| posted 15 Sep, 2016 17:51
Any Mac people who can help me with some basic WINE setup?
Shallee
pages@franklinpierce.edu
Posted in: SEA-PHAGES Virtual MachineWINE