Link to this post | posted 05 Aug, 2016 15:29

jross1025

As I guess many/most of us do, we make top agar in two components: a 2XL agar and what we refer to as a "fluid" portion which is just 7H9. We have a fair bit left over from last fall that was probably made back in late October. Does anyone have a handle on the shelf life of this stuff at room temperature? I'd hate to throw it out if it's still perfectly good, but it concerns me because I think it contains a fair number of low molecular weight organic compounds that may not do well in solution over time.

Link to this post | posted 13 Apr, 2016 19:42
jross1025	Thanks for the advice, it (emailing) worked perfectly!

Link to this post | posted 13 Apr, 2016 15:41
jross1025	Lee Hughes Fastest way: E-mail it to yourself from inside the VM. There are other solutions, but that is the simplest. Lee Lee: Thanks but I have no idea how to do that, can you run me through it? joe

Link to this post | posted 12 Apr, 2016 20:29
jross1025	I'm going to post this both here (on the VM thread) and on the Starterator forum since I'm not quite sure where it belongs. Earlier I ran a starterator report on our whole phamerated genome (LilDestine). Now I want to get it saved to my regular desktop (i.e. outside the VM) so that I can post it on a Blackboard site for student access. How do I do this?

Link to this post | posted 12 Apr, 2016 20:28
jross1025	I'm going to post this both here (on the VM thread) and on the Starterator forum since I'm not quite sure where it belongs. Earlier I ran a starterator report on our whole phamerated genome (LilDestine). Now I want to get it saved to my regular desktop (i.e. outside the VM) so that I can post it on a Blackboard site for student access. How do I do this?

Link to this post | posted 09 Mar, 2016 20:05
jross1025	Thanks again, Dan, this is helpful!

Link to this post | posted 03 Mar, 2016 17:28

jross1025

Dan: Thanks once again for helping out! I think my main problem is perhaps I don't quite understand what 1/1 alignment actually means. I thought it simply meant for example query=ala-ala-gly-gly-phe-met-met-etc target=ala-ala-gly-gly-phe-met-met-etc, in other words the sequences are same from beginning to end (maybe off a bit here and there) WHEREVER IT IS THEY ACTUALLY START IN THE SEQUENCE, so query could start at 14456, target could start at 14471, and they're still 1/1 aligned. Whereas say 1/4 alignment would mean something like query=ala-ala-gly-gly-phe-met-met-etc target=aa-aa-aa-ala-ala-gly-gly-phe-met-met-etc, so the aligned region in the target starts at aa#4 and continues from there until whenever, in other words the region of alignment is just sort of shifted 4 aa down. Should we just assume that 1/1 alignment means actual start site agreement?

Link to this post | posted 03 Mar, 2016 15:49

jross1025

Maybe I'm missing something obvious, but I really don't see how BLAST results can be used to validate (or call into question) a proposed start site. I understand the concept that perhaps moving the start can result in better BLAST (more hits, more 1/1 alignment, higher scores with lower E values etc) but what is it that people look at to determine that BLAST supports a start at, say 14639bp as opposed to a start at 14651? Or am I just fundamentally misunderstanding something?

Link to this post | posted 18 Feb, 2016 18:49

jross1025

Hi All: In tooling around on our genome just now, I saw something (below) in a BLASTp alignment within DNAM that I've never seen before: PGWRDIVATA GFGRXXXXXX XXXXXXEVTV ASGASHTAQL LVEGDNGINY 201 |||||||||| |||||||||| ||| || ||| |||||||||| |||||||||| 201 PGWRDIVATA GFGRALTALT ITPNAPSVTV ASGASHTAQL LVEGDNGINY 251 TPDCTFESSD PLKASVSAN 251 |||||| ||| | ||+|||+ 251 TPDCTFVSSD PTKATVSAS What do the X's mean? You have to mentally scoot the top line over a few spaces to line it up properly, but even still it's interesting that it recognizes some of the Xs as an identity to the target and some not. I've never seen this before. This is from LilDestine, in the product from the ORF that DNA Master calls starting at bp9002. It's a tail protein according to BLASTp at least.

Link to this post | posted 06 Feb, 2016 20:27

jross1025

I seem to recall that we ran into this last year as well but don't remember what if any resolution was achieved. We started trying to use phamerator just this past Thursday, on 16 HP machines running the 2016VM in a Windows 7 background. After starting phamerator in the VM and allowing it to complete the updating process, most students were able to see our relatively recently added phage (LilDestine, added last month[?]) but a few were not. It simply was not available in the list that one obtains upon clicking on "phages". At lower left, the student's screen would say "database update complete" or words to that effect. Any thoughts?