COMBOSA3D is used to color a three-dimensional representation of a protein according to the results of a sequence alignment. The program accepts a group of pre-aligned sequences in FASTA format (one of the sequences must have a solved three-dimensional structure), and it uses the alignment information to highlight conserved residues on the molecule.
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Bioinformatics. 2001 Feb;17(2):198-9.
COMBOSA3D: combining sequence alignments with three-dimensional structures.