Hi,

I am writing a custom extension based on MultiAlign Viewer that highlights regions in a multiple sequence alignment based on numerical values stored in an external file. I modified the RegionBrowser.py script, and added a function that works just like "showSS". It works fine for one structure and sequence combination. However, I am trying to associate multiple copies of the same protein structure and its sequence. So, the structures are identical and so are the sequences in the sequence alignment, but each copy represents different information. My problem is that the sequences in the alignment viewer dialog box are highlighted in a random fashion. And, I want the sequences to be highlighted in an ordered fashion starting from first sequence to last sequence since we want to be able to map the highlighted regions back to the external file.

Is there a way to control the order in which the sequences are highlighted in the alignment viewer dialog? Or is there a way to get the model # associated with a particular sequence and using the model # to highlight the alignment viewer?

I would highly appreciate your help.
Thank you,
Karan Uppal
Application Developer
Emory University


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