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I have project where I am required to build a visual analytics tool into an existing Java project to visually compare and analyse protein sequences from SwissProt, GenBank, EMBL etc. (downloaded from the databases in plain text and locally converted to XML)

Assuming I have the XML files of the protein sequences already, I am unsure regarding the following:

  1. The best ways to visualize protein sequence differences. (e.g. what types of graphs/ diagrams? Any sample images or links I could reference from?)

  2. What information should be derivable from these visualizations and how they help researchers.

Any advice on the above?

Note: I have no background in bioinformatics.

Any help would be greatly appreciated!

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    $\begingroup$ jalview is one possibilty : www.jalview.org $\endgroup$ – gilleain Dec 30 '20 at 19:42

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