Link to this post | posted 11 Feb, 2016 23:00
GregFrederick@letu.edu	Chris. Thanks for all the work on bug fixes in Starterator. (I'd send you a PM if I knew how in this system.) Could I persuade you to run Gideon_Draft on your version of Starterator for us and send me a link to the report? I promise to buy you a cup of coffee the next time we are at an HHMI function together!

Link to this post | posted 11 Feb, 2016 22:54
GregFrederick@letu.edu	GenMarck smeg Coding Potential for the region. 65Kb

Link to this post | posted 11 Feb, 2016 22:53

GregFrederick@letu.edu

In one genome we are seeing overlapping ORFs at the right end of the genome that are curious. See the attached file. DM actually called the long ORF on the reverse ORF and it is in some finished genomes too. But the first called forward ORF in the attached image actually has homologs with known function. The second forward ORF (indicated by the narrow bar) that was not called by DM actually matches with 9 other finished phages on PhagesDB. Question: Is it possible to have a large ORF like this spanning the COS site 'ends'? We BlastP'd it and even though some annotated phages include it, we do not find any putative function. I cannot seem to attach two files here. So I will attach the Genmark coding potential in a second post. Thanks for your thoughts. 23Kb

Link to this post | posted 10 Feb, 2016 19:00
GregFrederick@letu.edu	(I think if you click the broken picture link it will open a shared image from dropbox.) If not, it's attached here. 18Kb

Link to this post | posted 10 Feb, 2016 18:56
GregFrederick@letu.edu	When running Genemark on one of our phages the output had a blackened triangle near the coding potential line. I'm sure we were probably told during the annotation training… but I've lost it. Can someone please tell me what this indicates? Thanks in advance. Greg (I think if you click the broken picture link it will open a shared image from dropbox.) Edited 10 Feb, 2016 18:58

Link to this post | posted 10 Feb, 2016 17:10
GregFrederick@letu.edu	cdshaffer Both Andies and Willsterrel appear to have issues that have already been solved as both ran fine on my copy with my bug fixes, links to full reports below: Full starterator report for Andies Full starterator report for WillSterrel That is awesome! Thanks Chris! Is your newest debugged version of Starterator available for distribution?

Link to this post | posted 09 Feb, 2016 14:18
GregFrederick@letu.edu	Here it is from Dan's post on "Databases and Alternate servers" in this forum group… Server: http://phamerator.webfactional.com/databases_Hatfull Database: Actino_Draft Thanks for the heads-up on the "forced update".

Link to this post | posted 09 Feb, 2016 14:16
GregFrederick@letu.edu	Ahhh. I just checked on my notebook which does update and I found the following settings: Server: http://phamerator.webfunctional.com/databases_H (cannot see the rest!) Database: Actino-Draft I think I saw the correct server info listed in another thread… I'll go digging.

Link to this post | posted 09 Feb, 2016 13:55
GregFrederick@letu.edu	Thanks. I tried this and it does not seem to update on some computers. On the computers that are not updating I am seeing: Server: http://phamerator.csm.jmu.edu/sea Database: Mycobacteriophage_Draft I'm start to think these are not the correct server/database settings. Can you please confirm? Thanks. Greg

Link to this post | posted 08 Feb, 2016 19:58

GregFrederick@letu.edu

In several instances on several computers, Phamerator is reporting that it has the newest update. But it is unable to locate phages newly added to the database. We have tried restarting, switching in and out of phamerator and other apps in the VM, and completely restarting the VB. None seem to help. Is there a way to force Phamerator to run an update even though it thinks it has the most recent version avialable? Thanks in advance. Greg