Substitution matrix based color schemes for sequence alignment visualization

摘要

Typically, visualization of multiple protein sequence alignments colors the amino acid symbols according to some kind of (chemical) property. Examples for software using this visualization technique are [ ], [ ] or [ ]. Figure  shows an alignment using the default color scheme depicting the chemical characteristics of the amino acids. Typically, such a color scheme is created manually by a professional using their intuition and knowledge about any characteristics to be emphasized.