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Jalview: Coloring your aa alignment by functional similarity?

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#1 plasmodel



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Posted 23 January 2013 - 12:11 AM


I have done some aa alignment of four different proteins. Now, I want to color annotate that such the identical amino acids will be in X color and functionally similiar amino acids in a different color. How do I do that?

Jalview has color by percentage identity where it colors based on whether all the sequences have the same amino acid etc but I want something (and have seen it on papers) where they color residues based on functional similarity (so V, I, L may be colored if they are at the same position on different proteins0.

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