Link to this post | posted 23 Dec, 2016 00:31

lhughes

Quick question about PhamDB databases. I have successfully installed it on my machine now (rather than using Dan's web-access version). However, all the phages show up as "singleton" in my database. I am presuming that the Genbank files don't include cluster information, so that is why there is no cluster information. Anyone know how I could edit the GB files so that they include the appropriate cluster information when I load them into PhamDB to generate a Phamerator database? Thanks, Lee

Link to this post | posted 05 Aug, 2016 00:20
lhughes	Chris: Just tried it on my machine as well. It stayed on version 1.1.0 and I definitely had internet connectivity in the Virtual Box. Even opened, closed and then reopened Starterator Beta to see if there was any change. Lee

Link to this post | posted 30 Jul, 2016 17:54
lhughes	Ok - tried Sprinklers again in Beta after clearing Intermediate files. It worked then. Sorry I didn't try that the first time. Lee

Link to this post | posted 28 Jul, 2016 20:48
lhughes	Chris: I am running the Beta version of Starterator on a phage that I am doing QC on and it is failing. The phage is Sprinklers (C1) and it fails on Pham 192 of 232. Thanks, Lee

Link to this post | posted 27 Jul, 2016 01:20
lhughes	I like the gray scale/red font options. That comes across very easy to see. As Welkin mentioned, when there are too many starts (or too many tracks) it gets really hard to see anything. The font size example doesn't work as well (to me) as the 1st option did. Thanks for working on this! Lee

Link to this post | posted 24 May, 2016 16:50
lhughes	I will always remember David's infectious smile and the sincere joy and excitement he brought to our discussions of science and learning. He will be sorely missed. My thoughts go out to his colleagues, friends, and family.

Link to this post | posted 27 Apr, 2016 16:03
lhughes	Yes - that is it. It is really good for making small custom databases (I've used it to look at just Streptomyces genomes). I don't think you'd want to use it for a full database though because that would take quite a long time and use a lot of computing resources. Lee

Link to this post | posted 27 Apr, 2016 01:03

lhughes

Greg - are you just trying to align with similar phage? You can do that pretty simply by creating a small database and using the web-based tool that was mentioned previously in the forum. You can also do a similar gene length alignment using DNA Master and the Genome Comparison tool with a few select phages for comparison. Would either of these accomplish you overall goal? Putting together a custom Phamerator database for all the phages is a pretty large job. Lee

Link to this post | posted 13 Apr, 2016 18:34
lhughes	There is a Chrome browser on the program menu in the VM (it is usually just above the Phamerator icon). Just open Chrome and use any web-based e-mail program to attach the file and e-mail it to your own e-mail address. Lee

Link to this post | posted 13 Apr, 2016 02:47
lhughes	Fastest way: E-mail it to yourself from inside the VM. There are other solutions, but that is the simplest. Lee