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Occasionally I will run protein alignments on peptide families and I can never remember what the symbols mean to show degrees of identity. What do they mean?

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From the FAQ for the Clustal-W2 program:

An * (asterisk) indicates positions which have a single, fully conserved residue.

A : (colon) indicates conservation between groups of strongly similar properties - scoring > 0.5 in the Gonnet PAM 250 matrix.

A . (period) indicates conservation between groups of weakly similar properties - scoring =< 0.5 in the Gonnet PAM 250 matrix.

Therefore the hierchy of conservation using these symbols is * (identical) > : (colon) > . (period).

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