SEA-PHAGES | All posts created by rdejong

Link to this post \| posted 27 Feb, 2024 18:02
rdejong	Like fbaliraine (Fred) we have a possible minor tail protein called very early (gene 4) in our phage that is called a minor tail protein in a similar gene (JFlix 2). Unlike the previous post, we have no correlation to any gene with any canonical orientation. We ended up calling this gene minor tail protein in Jflix2 last year, but not finding anything in our notes why - it may have occurred during the QC process. Guidance would be appreciated!

Link to this post | posted 27 Feb, 2024 18:02

Like fbaliraine (Fred) we have a possible minor tail protein called very early (gene 4) in our phage that is called a minor tail protein in a similar gene (JFlix 2). Unlike the previous post, we have no correlation to any gene with any canonical orientation. We ended up calling this gene minor tail protein in Jflix2 last year, but not finding anything in our notes why - it may have occurred during the QC process. Guidance would be appreciated!

Posted in: Functional Annotation → Minor tail proteins far upstream of the tape measure protein?

Link to this post \| posted 10 May, 2018 19:14
rdejong	I have some students that wish to finish annotating genomes into the summer. The following question has come up for two students who have installed DNA Master on their own PC. They have been successful in getting DNA Master to update as well. The program is working except that in the Frames view, when the RBS data function is used, it only displays one set of measurements of RBS strength ('Shine Delgarno score and SD space'. The options to choose Z scores and Kibbler scores and the like are not there. Why might they be missing (new version?) and is it possible to get them back? I hesitated to start this as a new topic but I did not find any answer to this issue within any of the other threads. Thank you!

Link to this post | posted 10 May, 2018 19:14

rdejong

I have some students that wish to finish annotating genomes into the summer. The following question has come up for two students who have installed DNA Master on their own PC. They have been successful in getting DNA Master to update as well. The program is working except that in the Frames view, when the RBS data function is used, it only displays one set of measurements of RBS strength ('Shine Delgarno score and SD space' smile

. The options to choose Z scores and Kibbler scores and the like are not there. Why might they be missing (new version?) and is it possible to get them back?

I hesitated to start this as a new topic but I did not find any answer to this issue within any of the other threads.

Thank you!

Posted in: DNA Master → DNA Master and RBS data

Link to this post \| posted 10 May, 2018 19:00
rdejong	Thanks Kristen! We'll give it a try!

Posted in: DNA Master → Running DNA Master on a Mac using Wine

Link to this post \| posted 10 May, 2018 01:14
rdejong	This will hopefully be a silly, easy-to-answer question! We don't typically use DNA Master for Mac in our course, but we have some students who wish to continue unfinished annotations into the summer. They have downloaded and installed the Wine Bottle version posted by Baylor (thanks SEA colleagues!), and it appears to run fine. However, some run into trouble in that they cannot open files - they just hang. My suspicion is that the files need to be in the DNA Master archives folder, only those files aren't 'seen' when in the Mac Finder. Is my suspicion correct or is something else? Any solutions? Thanks!

Link to this post | posted 10 May, 2018 01:14

rdejong

This will hopefully be a silly, easy-to-answer question!
We don't typically use DNA Master for Mac in our course, but we have some students who wish to continue unfinished annotations into the summer. They have downloaded and installed the Wine Bottle version posted by Baylor (thanks SEA colleagues!), and it appears to run fine. However, some run into trouble in that they cannot open files - they just hang. My suspicion is that the files need to be in the DNA Master archives folder, only those files aren't 'seen' when in the Mac Finder. Is my suspicion correct or is something else? Any solutions?

Thanks!

Posted in: DNA Master → Running DNA Master on a Mac using Wine

Link to this post \| posted 20 Feb, 2018 20:10
rdejong	I have the same question as Greg, regarding the need to make notes about HHPred findings if BLASTP gives a strong function ID.

Posted in: Notes and Final Files → Documenting Gene Calls in DNA Master

Link to this post \| posted 22 Jan, 2018 19:43
rdejong	Dan Russell, I am having a real issue with getting 2017 SEA VM working on our Windows 10 computers. Can you get me the 2016 SEA VM that is 32 bit? Cal Keen ckeen@calvin.edu

Posted in: SEA-PHAGES Virtual Machine → Student download of 2016 VM

Link to this post \| posted 24 May, 2016 20:10
rdejong	So shocking because he was such a vibrant individual. He had remarkable enthusiasm and love for science, students, and fun. He was always a joy to interact with and he will be terribly missed in the SEA. We at Calvin offer our prayers and sympathies to his family and to the Cabrini community. Edited 24 May, 2016 20:44

Posted in: Messages for Cabrini College → Messages for Cabrini College

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All posts created by rdejong