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. Author manuscript; available in PMC: 2021 Jul 17.
Published in final edited form as: Methods Enzymol. 2020 Jul 17;643:149–179. doi: 10.1016/bs.mie.2020.06.001

Figure 1. Extracting a consensus sequence from a multiple sequence alignment.

Figure 1.

(A) An alignment of M=4,571 homeodomain sequences, each of length L=57 residues. Residues with similar (or unique) chemical features are highlighted to illustrate conservation. Positions with a gap in more than half the sequences are eliminated from the alignment. From such an alignment, the frequency of each type of residue (including remaining “gap residues”) is determined. (B) The consensus sequence (bottom) is obtained by taking the residue with the highest frequency (excluding gaps, see Section 3) at each position (red).