Link to this post | posted 22 Jan, 2018 23:21
smolloy123	Hi Tamarah, It sounds like some of my PC students are having this problem too. They are able to open the program but not update. Here is a screen shot (attached) of what one PC student sent to me. Thanks! Sally 143Kb

Link to this post | posted 22 Jan, 2018 16:48
smolloy123	Hi Claire, Does it take a while for starterator and pham data to appear on the site? Over break I annotated a large number of genomes on Pecaan and don't remember it taking a long time for this data to appear. It has been at least a week since I entered five new genomes and the HHPRED and BlastP data is there but not the starterator/Pham data. Thanks! Sally

Link to this post | posted 05 Jan, 2018 13:55

smolloy123

Hi All, I know there are typically 5 minor tail proteins after the tape measure gene. But are we also calling the three short genes within the minor tail proteins (gp 29, 30 and 31 in NeruJay, see top phamerator genome in attachment screen shot) minor tail proteins? gp30 and 31 are at least membrane proteins but there is no HHPRED evidence for minor tail proteins. Is this a situation where following phamerator is the right thing to do or would I be perpetuating bad calls? Thanks! Sally 146Kb

Link to this post | posted 02 Jan, 2018 14:04
smolloy123	Hi Welin, Thanks! I suggest "lysin A, peptidoglycan binding domain."

Link to this post | posted 31 Dec, 2017 19:50

smolloy123

Hi All, I have a question about split lysin A genes in the CR1 genomes versus the DM genomes. In Flapper, a cluster CR1 genome, the call was pretty straight forward as the HHPRED matched up wtih the approved functional calls "lysin A, protease M15 domain" and "lysin A, glycosyl hydrolase domain" for Flapper proteins gp52 and 53 in phamerator. But in SallySpecial, a DM phage, the two genes gp5 and 6 are more like the two genes in Strept phage C1 that has Lysin A gene product that encodes the peptidoglycan binding subunit and a second gene that encodes the catalytic gene. I called these genes using the approved functions but in hind sight I don't like the gp 5 call as the protease M15 domain. I attached the HHPRED results of the two SallySpecial genes. Any insight on this Welkin or Veronique or anyone? Thanks! Sally 756Kb

Link to this post | posted 31 Dec, 2017 16:45

smolloy123

gp 23 in Flapper, a CR1 phage, has a decent match in HHPRED (99% prob, 46% cov, 8E-18 eval) with a tail spike protein (tailspike gp27; Beta-helix, tailspike, Lyase; HET: NA, ACT, EDO; 1.52A {Pseudomonas phage phi297}). This is not an approved function. Yet I also found this gene called as such in SuperSulley (gp22), a CR2 genome. Veronique QC'd this genome and she is one of most experienced SMART members, so is this an approved function? Veronique or Welkin have any thoughts on how to call this gene? Thanks!

Link to this post | posted 29 Dec, 2017 15:05
smolloy123	Hi Dave, Good to know it isn't just me Today, Phamerator "ain't misbehavin'" The nucleotide identity colors are back in order and I can move back and forth between PECAAN and phamerator pages without any crashes. thanks! Sally

Link to this post | posted 28 Dec, 2017 17:57

smolloy123

Hi, just wondering if others were having trouble with web phamerator. Every time I move to a different web page (i.e. PECAAN) and come back to phamerator it is frozen. I can't just refresh the page, I have to close the page, add a new page, go to phamerator etc and remap every time I want to look at a gene. Also, it doesn't look like there is nucleotide identity shown between the genomes. I have been using the web phamerator since last spring and I haven't experienced this before. Thanks, Sally

Link to this post | posted 09 Dec, 2017 21:20

smolloy123

Rodney King Has anyone experienced degradation of DNA isolated by the new protocol? We tried a brand new DNA isolation kit and brand new enzymes and still see degradation. Never experienced this problem before. The fact that the DNA disappears only in the presence of restriction enzyme buffer indicates DNAse is not being thoroughly removed. Hi Rodney, We experienced this although two things to point out. We used phenol chloroform extractions and did not use Promega kit, treated lysates with EDTA after DNAse and RNAse treatment. I would think that the phenol chloroform would do the trick although maybe we needed to do two extractions in a row? Also, our DNA degraded only in certain restriction endonuclease reactions and not all the reactions.

Link to this post | posted 28 Jul, 2017 21:17

smolloy123

Hi All, This is a QC question. I have a DNA Master file I just finished QCing and the translation table was standard rather than bacteria and plant plastid. I am assuming they forget to change this in the settings when they did the auto-annotation. When I make the flat file I choose Bacteria Plastid etc but does it matter that the DNA master file that I post on phagesdb has the standard translation table? Thanks! Sally