COMBOSA (Coloring Of Molecules Based On Sequence Alignment) 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 aligned sequences in FASTA or GDE format (one of the sequences must have a solved three dimensional structure), and it generates a script that can be used by a molecular visualization program (RasMol). The script adjusts the color and appearance of the molecule so that conserved residues are highlighted.

Paste the aligned sequences (in FASTA or GDE format) into the text area below. If you include the solved sequence in this text area the identity and similarity calculations will include the solved sequence.

Paste the aligned solved sequence into the text area below (be sure to include the sequence title). The script that is generated should only be used when examining the structure of the molecule described by this sequence.

Use the following two selections to alter the appearance of the accompanying multiple alignment figure.

  • Show residues per line.
  • Use text.

Choose the colors you wish to use for highlighting. Gaps (amino acids in the solved sequence that align with gaps in the other sequences) have the highest priority for coloring, followed by identical amino acids, and then similar amino acids.

  • Color gaps , identical amino acids , and similar amino acids
  • Percentage of sequences that must agree for gap, identity, or similarity coloring to be added:
  • The default color (the color used if no gap, identity, or similarity coloring is added):

Enter the groups of similar amino acids separated by commas to be used for the similarity calculation.