Link to this post | posted 05 Apr, 2016 17:14

cdshaffer

According to the phamerator map, the wrap around gene is pham 9781 I cannot find any proteins in pham 9872 so I am going to guess you have a typo when you put 9782. If that is not the case let me know, I will chase down this discrepancy (could be an issue with a database and be causing the crash). Proceeding with the analysis based on the typo assumption, I can confirm that Tonenili crashes for me on the wrap around gene. I am going to run the version of the program which should skip that gene. These runs take a while I will post again when I have results. Edited 05 Apr, 2016 17:31

Link to this post | posted 04 Apr, 2016 21:49
cdshaffer	Tonenili is a C1 phage, I bet there is a wrap around gene which is causing the crash. I have a version of starterator which tries to recognize this situation and just skip the analysis for that gene. Analysis is running now. I will try running on that version of starterator and see if we can avoid the crash. I will post an update one way or another as soon as I can Edited 05 Apr, 2016 17:01

Link to this post | posted 16 Mar, 2016 20:31

cdshaffer

My own feeling is that coding potential is a good positive signal but a lousy negative signal. That is, seeing coding potential is a good sign for the presence of a gene but no coding potential is not good evidence for the absence of a gene. Coding potential is mostly about matching the nucleotide biases of the genes in the training set (be it self training on the phage itself or trained on a nearby host). Its always possible that a gene has evolved for some reason to specifically NOT match a particular bias. Say expression in a different host for example, or evolved for slow translation rates by using rare codons. In addition, I was trained that when in doubt it is always best to over annotate, not under annotate. The idea was it is better to have a false positive protein in a database than a false negative protein missing from the database. Its typically easier to find and reject an error than it is to find something that has been erroneously left out. Having said that, I will mention that the first point is my own opinion and I would not be surprised if other reasonable annotators disagree. Its really about data interpretation without guidance from any experiments so its all about opinion. As for the later point, I have found that policy to be much more a consensus in the community of human annotators that trained me and much less so in the community of people I have met that work with prokaryotes. So a reasonable counter argument is that it is better to match the standards of the community to which I would defer to others to voice an opinion.

Link to this post | posted 12 Mar, 2016 02:47

cdshaffer

TyrionL ran fine on my computer with the normal version of Starterator. This suggests that you may have a corrupted database or some other issue with your copy of the virtual machine. If you need to run a bunch more phage through Starterator you may want to re download the virtual disk and reinstall. If you just have a small number of other phage to do, just post them here I am happy to run them, the only issue really is the slow turn around time since I can get busy and not check the forum for days. You can download the full report for TyrionL from this link.

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.