Link to this post | posted 05 Feb, 2019 19:49

Pollenz

On further review I was thinking Emperor could be a prophage…….this is posted on the Emperor Phages DB: Emperor was found as a prophage of Gordonia westfalica NRRL-B-24152. Liquid Gordonia westfalica was spotted on Gordonia terrae 3612, and the resulting phage release was picked and amplified, and called Emperor. So, now it make sense and perhaps since the Emperor genes are redundant to the Gordonia genome genes, they do not hot when doing a BLASTP. RS Pollenz

Link to this post | posted 05 Feb, 2019 14:31

Pollenz

We are currently annotating a DM phage, Ashton. This cluster has few members and Ashton is from M. foliorum while the others are from Gordonia terrea. Ashton has some nucleotide similarity to SallySpecial and Emperor and there are high and low areas as you would expect. In the BLASTP analysis, we are not consistently seeing the genes from Emperor as hits but getting hits to proteins from Gordonia westfalica as the top match when we expect to see products from Emperor. When I do a BLASTP on the products from Emperor, they all hit with 100% alignment and 100% identity to Gordonia westfalica (the genes from Emperor are NOT showing as hits), even Emperor gene #9 listed as an orpham (see screen shot) hits to the westfalica! I can also manually align Ashton and Emperor products to show alignments that NCBI is not showing me vs giving me the Gordonia westfalica hits. Emperor is in Genbank, so I can find the sequences and accession numbers. Am I missing something here? Why is Emperor phage 100% matching to an annotated bacteria genome from a different Gordonia strain? We do see hits to the SallySpecial products even though they have much reduced identity vs. Emperor in some instances. RS Pollenz 412Kb

Link to this post | posted 04 Feb, 2019 20:03
Pollenz	OK great. Here is another interesting situation. We have a double start codon GTGATG where the GTGA creates the 4 bp overhang to to the previous gene. I know from Welkin that we typically choose the 2nd start codon if there are two consecutive……Thoughts since choosing the ATG is a one bp overlap to the TGA stop. The RBS data show identical values for the GTG and ATG. RS Pollenz

Link to this post | posted 22 Jan, 2019 17:14
Pollenz	I see mention of the ATGA 4bp overlap across 2 genes as a preferred configuration and can assist in selecting a correct start site. What is the situation with a GTGA 4bp overlap? We have several genes in our EE phage that show this GTGA configuration. Is this also a preferred orientation that should be noted in the annotation notes file? RS Pollenz

Link to this post | posted 08 Jan, 2019 18:40
Pollenz	Thanks, I have class at 3:30 so will hopefully get it all configured. RS Pollenz

Link to this post | posted 08 Jan, 2019 14:18
Pollenz	We have our first class today and I have not reviewed the issues directly, but I have several emails from students saying "We can get to the setup wizard just fine, but once you hit finish which should open the actual program, it shuts down and wont open." Suggestions? RS Pollenz

Link to this post | posted 14 Dec, 2018 12:31
Pollenz	I was using the program up until December 12, 2018 and for the past few days I am unable to access the site from any computer or browser. Is the site down? The message I am getting is "Unable to Connect". I have used Chrome, Firefox, Safari and get the message across all browsers and tried access from my home and office desktop. Thank you RS Pollenz

Link to this post | posted 15 Jun, 2018 10:33
Pollenz	Ok, thanks to all and the version is correct and settings are also correct. When I hit blast this gene it returns: Cannot load SSL library with a big X RS Pollenz

Link to this post | posted 13 Jun, 2018 15:33
Pollenz	Thanks Dan, the version i have is updated, but where do i see the info above about the build, i dont see it in the preferences. I can say that the secure window does not look exactly like the notes I saw as its missing one of the check boxes. I also am getting a "cant load SSL library when I tried to blas a single gene. RS Pollenz

Link to this post | posted 13 Jun, 2018 14:42
Pollenz	Madison and I tried this but we dont get the box about a secure connection after restarting we get the what do you want to do box. RS Pollenz