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All posts created by stpage
| Link to this post | posted 19 Feb, 2021 17:30 | |
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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 Master → DNA master server down?
| Link to this post | posted 09 Mar, 2020 20:24 | |
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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 Annotation → ribonuclease function
| Link to this post | posted 03 Mar, 2020 20:43 | |
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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 Tips → Tail Assembly Chaperone
| Link to this post | posted 03 Mar, 2020 17:15 | |
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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 Tips → Tail Assembly Chaperone
| Link to this post | posted 02 Mar, 2020 01:48 | |
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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 Tips → Tail Assembly Chaperone
| Link to this post | posted 23 May, 2019 22:05 | |
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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… |
Posted in: Cluster BD Annotation Tips → DNA Primase
| Link to this post | posted 23 May, 2019 01:38 | |
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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 Tips → DNA Primase
| Link to this post | posted 11 Apr, 2017 18:14 | |
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The last couple of days, I can't open the Lawrence Lab web page to download DNA master… |
Posted in: DNA Master → DNA Master failed update
| Link to this post | posted 06 Oct, 2016 17:09 | |
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Thanks, Dan. (And, the direct link to SEAVM helped a lot too) |
Posted in: SEA-PHAGES Virtual Machine → WINE
| Link to this post | posted 15 Sep, 2016 17:51 | |
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Any Mac people who can help me with some basic WINE setup? Shallee pages@franklinpierce.edu |
Posted in: SEA-PHAGES Virtual Machine → WINE