Link to this post | posted 07 Mar, 2016 16:47
cdshaffer	Just an FYI, you can create the genbank files you need by using the DNA Master "Submit to GenBank" tool which, not surprisingly, is found in the Tools menu.

Link to this post | posted 04 Mar, 2016 18:02

cdshaffer

The only graphical way to do this is the recently published PhamDB (see my post in starterator). If you want to go the traditional route, updating the database requires using the python scripts posted by Charles Bowman at his bitbucket repository for k_phamerate. K_phamerate uses a set of programs for database creation that are incompatible with the version of Ubuntu running on the sea-phages virtual machine so you need a different machine to manage databases. I have a virtual machine with all the k-phamerate code installed that I can get to you if you want. This machine is quite a bit larger at almost 12 Gig. So it is not a trivial undertaking. Edited 04 Mar, 2016 18:03

Link to this post | posted 04 Mar, 2016 17:24

cdshaffer

Starterator does have the "One unphamerated gene" routine which you select from the menu that always starts with "Whole phamerated phage". Starterator asks for the name of the phage, the full fasta sequence file, and info on the gene (coordinates and strand) you would like to analyze. I have only looked at the code for that routine briefly but it is clear that starterator is extracting the region of interest, doing some calculations to guess the pham it would be in, and then running the starterator analysis. Unfortunately, my students and I have only had limited success with that particular routine. I gave up using it in class. It appears to work on some phage/genes but not others. So you can certainly try it and if you get a report, great. If not, the only solution I know of would for either you or someone you know to create an updated phamerator database with your improved annotations so you can do a whole gene report in starterator. Phamerator database creation is typically done with unix, python and sql command line but Randal DeJong just published a web based system for phamerator database management called phamDB. Once you get it set up (still not trivial but certainly easier than command line phamerator) you can easily remove/add/update phage in your database. Here is the link to the bioinformatics paper. Oh, and by the way, Congratulations Randal! He presented preliminary work on this at the last symposium and its nice to see it has now been published. Edited 04 Mar, 2016 17:26

Link to this post | posted 02 Mar, 2016 16:43

cdshaffer

Sangha, I can confirm that phage PhancyPhin also crashes on my machine when running the current version of starterator so I don't think there is anything wrong with your computer. I was able to run is successfully with my updated code so the problem was an old bug in starterator that we have found and fixed. You can download the full report using this link. Thanks for reporting the issue, the only way to make programs better is if people take the time to post problems that can be checked.

Link to this post | posted 02 Mar, 2016 16:25
cdshaffer	David: Lucy and Vallejo reports

Link to this post | posted 27 Feb, 2016 17:16
cdshaffer	David, My bad, I mis-clicked on the permissions and only shared with other WashU people, so I think the "fee" to get access would probably be more properly termed "tuition". I don't think we want to wait that long so I changed permissions, RcigaStruga should now be available from the link above to anyone. Here are the links to the other reports, easy peasy. Christian, Huntingdon, Canowicakte.

Link to this post | posted 26 Feb, 2016 20:31

cdshaffer

Don't worry too much about time. It takes me about 3 minutes to start the run (then the computer works on its own) and about 5 minutes to post the results if they work. If they don't work and still crash starterator then I really do want to document that so we have as complete a list as possible of potential bugs. I got Suppi and RcigaStruga to work just fine with my updated code. I then tried with the original version of Starterator without my code updates and Suppi worked there as well. So now I wonder if this is something specific with your machine. See the sticky first message in the starterator section on common troubleshooting, you should in particular try to delete all the cached Intermediate files (item 2) as that can cause problems if you try to run starterator on phage and the phage get updates in the database. If your phage are still crashing I wonder if you have a corrupted database. You might want to try opening phamerator and doing a force database update. Also try a couple of machines see if you get crashes on only one or all of them. If all those don't help let me know, I can post more reports. easy enough to do over the weekend.

Link to this post | posted 26 Feb, 2016 16:22

cdshaffer

Nancy, It looks like Starterator was crashing on LouisV14 for an already solved problem, as my local version of starterator with my added code worked just fine and I was able to make a full report. You can download the full report here. David, If I remember correctly the individual gene routine still needs a lot work Starterator crashes on many negative strand genes and if I remember correctly it also does not work well if you give it an orpham. Like you, my early experience in class was very sporadic, some genes worked others did not. Consequently I abandoned that routine in class pretty quickly and worked on getting the whole phage report working since that produced a PDF that could be used for the remainder of the semester. I have not worked on any bugs in the single gene routines at all really, instead, putting what time I could on the bugs that cause the whole phage report to crash. Can you send me the names of one (or two) phage and which pham was being worked on when starterator crashed. I am more interested in which phage cause crashes then doing a whole phamerated phage report as that (I think) is the most important routine to debug but any well documented reports of crashes are always welcome. As long as I get get them to repeatedly crash I can put them on the "to do" list of bugs to investigate and fix. Edited 26 Feb, 2016 18:33

Link to this post | posted 25 Feb, 2016 16:03

cdshaffer

I had the same issue with some of our recently isolated Streptomyces phage. Several of them were so novel across the whole genome based on BLASTn that I had to go the "find the terminase" route. Looking at some of the previous Streptomyces phage the terminase is not always the very left most gene, so I matched those phage and I ended up moving to the left several genes to find a "clearing" in the coding potential and then pick base 1 somewhere that would avoid dividing any long ORFs. You can look at phage Yara_draft in phamerator as an example. A few of our phage were similar to Yara so we used that as a guide. In Yara the similarity to terminase starts at around 2.5 kb and is the 8th gene called by DNA Master auto-annotation.

Link to this post | posted 24 Feb, 2016 21:16

cdshaffer

The pdf library in phamerator is not very good so if you save a map from phamerator directly to PDF and try to print in large form it does not work well. Here is the recommended protocol I give my students: 1. Open phamerator and create your map. 2. Edit the view menu to set what is shown and not shown to suit your purpose 3. Save as a SVG from phamerator. 4. Transfer the file as needed to a computer which has Inkscape installed. (Inkscpe is a free to download graphics program that works kind of like Illustrator. There are versions for all platforms) 5. Open the file in Inkscape and use save as… to save in PDF format 6. Open the PDF version of the file in whatever program you are using to create your poster 7. Typically students are using Powerpoint to create a giant slide, in which case I tell them to use the Insert menu -> photo -> picture from file to select the PDF. Then resize the map to fit the size of the poster.