The primary structure of a protein shows the mere sequence of amino acids. Color coding can be used to identify hydrophobic, sulphur-containing, acidic, or basic residues.

Alignments of such primary sequences can help to identify regions of interest in related proteins. Here, color coding has been used to depict conserved hydrophilic and hydrophobic stretches within the primary sequence.

Other applications might search for a given motif, a sequence of amino acids separated by others. By comparing to known structures, such motives might be identified already in the primary structure.