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All posts created by Pollenz

| posted 14 Jun, 2019 15:31
hello

I have a new 2019 DELL laptop and have been trying to install DNA master. I do not get all the files in the download (no library or ssleay32 files) and I do not see the DNAMas updated version showing up like I saw when I did this on an older machine I borrowed prior to the conference last week (running windows 7). Thus, the program that is downloaded will not update from the 2012 version. I tried form both Phages DB links and seaphages.org. I have uninstalled and tried several times but get the same results. I noticed that when I initially download the file and open in the downloads folder, the DNAmas.ex will not initially launch and gives an error saying that it will not run on a PC, but eventually the DNAmas.ex does turn into the DNA master icon so I can launch the installer……but only seems to contain the minimal files listed above.
RS Pollenz
Posted in: DNA MasterDNAS master install on 2019 PC
| posted 23 May, 2019 17:32
We have worked in Gordonia r. and M. foliorum the past few years. Typically, the uncut DNA from isolated that have high concentration (> 200ng/ul) runs with a high mol mass band, but does show some amount of smear (see enclosed example). The gels sometimes show a double band or gap in the high mol mass DNA. If we have low yield samples (<50ng/ul), they sometimes do not run as a high mol mass band and appear smeared but its hard to tell if that's because the concentration is already low and was degraded during the isolation.
RS Pollenz
Posted in: Phage BiologyDNA Smear
| posted 05 Feb, 2019 19:49
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
Posted in: AnnotationPhage hits not showing in NCBI but 100% to Gordonia wetsfalica
| posted 05 Feb, 2019 14:31
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
Posted in: AnnotationPhage hits not showing in NCBI but 100% to Gordonia wetsfalica
| posted 04 Feb, 2019 20:03
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
Posted in: Choosing Start SitesGTGA overlaps
| posted 22 Jan, 2019 17:14
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
Posted in: Choosing Start SitesGTGA overlaps
| posted 08 Jan, 2019 18:40
Thanks, I have class at 3:30 so will hopefully get it all configured.
RS Pollenz
Posted in: DNA MasterProblem installing DNA Master on Windows 10
| posted 08 Jan, 2019 14:18
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
Posted in: DNA MasterProblem installing DNA Master on Windows 10
| posted 14 Dec, 2018 12:31
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
Posted in: Web PhameratorIs Web Phamerator Down?
| posted 15 Jun, 2018 10:33
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
Posted in: DNA MasterImportant DNA Master Update