Link to this post | posted 08 Oct, 2015 17:28

cdshaffer

I would be happy to look into this. It is pretty unlikely that you are doing something wrong. To start I need to make sure I have the same database to see if I can replicate the problem. If you open up Phamerator and select Edit -> Preferences. You should see something like the picture I attached. Do you see the same Actino_Draft for the Database, or something else? If you do see Actino_Draft, can you check that your Ubuntu machine is able to get to the internet to download the most recent version of the database? To do that just open up a web browser in the ubuntu machine and see if you can get to sites on the internet like seaphages.org. Edited 08 Oct, 2015 17:33 36Kb

Link to this post | posted 24 Sep, 2015 19:59

cdshaffer

The fasta file from either source will work as input for another program but it can be a hassle if you want to see the sequences yourself. In that case you will probably want to reformat. On the web I use the EMBOSS tool called seqret to do that. Do a google search on "emboss seqret ebi" and pick the seqret server at www.ebi.ac.uk You can upload your fasta file and select "FASTA format" as the output format and all the sequences will be formatted so you can see the entire protein sequence without having to do so much horizontal scrolling.

Link to this post | posted 24 Sep, 2015 19:52
cdshaffer	In DNA Master: 1. DNA Menu, bottom item is "Save ORF's…" which will bring up the tool window 2. You will see a list of all the features in your phage 3. Select one or more by clicking, or use the "Select all genes" button 4. Go to the "Specify Export Files" tab 5. Use the checkboxes as appropriate to control what will be saved (e.g. "Peptide Sequences" 6. Click the "Save" button

Link to this post | posted 18 Sep, 2015 18:03
cdshaffer	Dan, Can you create a page that students can get to that has all the instructions for installing the machine just like on the protected /software/virtualmachine/ page? I would like to be able to point students to all those well written instruction on how to go about installing virtual machines once I give them the virtual disk I want them to use. thanks

Link to this post | posted 17 Sep, 2015 02:10
cdshaffer	Well, I cannot say if we are getting "good" infections. We haven't tried to titer a stock with the different plating techniques. What I can say is every pair of students has a phage from their soil samples. So it seems to be working well enough.

Link to this post | posted 16 Sep, 2015 16:40

cdshaffer

We are using top agar with lividans and getting good plaques. Students are simply spreading phage solution on the plate, then adding top agar onto the plate with the spores already added to the top agar. Very Convenient, since it avoids the 15 min incubation step we did with phage + mycobacteria. Always nice in a class setting with limited time. So far so good for us, looks like we have at least a dozen phage isolated by direct plating. The hard part is growing and collecting the spores it adds time to prep work but they are expected to be stable throughout the phage isolation and purification stage so we only have to collect spores once. Edited 16 Sep, 2015 16:43

Link to this post | posted 11 Sep, 2015 20:45
cdshaffer	Dan, could you post the MD5 hash of the two images. I would like to confirm the integrity of the files after download. Thanks Chris

Link to this post | posted 23 Jul, 2015 20:44

cdshaffer

I tried TymAbreu_draft but that phage was not found, I have the most recent version of the Actino_draft database and in there the phage is no longer "_draft", its just Tymabreu. so I tested it out. Phage ran with no crashes, the likely culprit is confusion between the different "_draft" and current versions of the annotation. I suggest you use phamerator to update the actino_draft database and delete all the files in "Intermediate Files" folder (see the other "troubleshooting starterator" post) then try again. That is likely to work. However in case you need it, I posted the full phage report here. You can download from that link if the above suggestions fail to fix the problem on your system.

Link to this post | posted 19 Jul, 2015 21:05
cdshaffer	more info on phage dori crash the last two genes in dori are problematic, for both of these genes there are no in-frame stop codons upstream of the annotated start codon all the way to the end of the phage. This appears to be causing the crashes. I am slowly working on how best to modify code with minimal risk of breaking something else. Edited 22 Jul, 2015 16:43

Link to this post | posted 16 Jul, 2015 03:37
cdshaffer	phage Amela_Draft from the Actino_Draft database has also been reported to crash starterator.