DNA and protein in the same view.

Adrian

• October 25, 2016 02:22

Hi,

 

I'm trying to create some new mutants and the best thing for that is to identify places where several strains differ. I have both the DNA and Proteins for several serotypes. 

I want to manually display and edit dna sequences and protein sequences. Snce they are both strings and 3 bases make a protein there should be a way to align them manually but there seems not to be a way in the current interface.

 

If I select DNA and protein documents the resulting view shows me only the text for both but I also want the sequence.

I could probably translate the proteins to have all as DNA but it gets messy when you have many sequences and editing that is most likely to change the frame.

I'm trying to do that in a plugin but it seems all the examples accept only one type or the other. That's similar to the existing interface and it does not cut it for the current goals.

 

 

Thank you,

Adrian

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  Richard Moir

  • October 25, 2016 02:50

  The ExampleDocumentViewerPlugin would be the place to start if you want to build it as a viewer. It accepts SequenceDocument which can be either protein or DNA. However, it needs to be extended to accept more than one sequence (and do all the rendering and allow editing appropriately).

  Building a plugin for this will be a lot of work, so I would recommend aligning all as DNA and using the live translation in the existing viewer to check your edits.

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  Adrian

  • October 31, 2016 09:50

  Hi Richard,

  I built the following viewer and that has some of the functionality I'm interested however I would need a lot of the functionality present in the Sequence Viewer and since reinventing the wheel is not fashionable I need to be able to subclass the Sequence viewer plugin and override some of it's functionality. Can you direct me to some documentation on how to do that? 

  I'm talking about subclassing the existing SequenceViewer.java and SequencePluging.

   

   

  

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  Richard Moir

  • October 31, 2016 20:53

  I'm afraid that's not possible, our sequence view has not been designed to be extended in this way. You will have to recreate the necessary functionality in your plugin.

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  Adrian

  • October 31, 2016 23:48

  Hi Richard,

  That's quite a limitation.

  Is there any way for instance to extend the existing one to add a new sequence or something like a Sequence Logo?

   

  I looked through the SequenceViewerStatistics but that does not modify the main Sequence Viewer panel but something on the side.

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  Richard Moir

  • November 01, 2016 01:25

  Yes, you can extend the sequence view in a couple of controlled ways. Have a look at GeneiousPlugin.getSequenceGraphFactories() as a way to add something like a sequence logo.

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