Gene Composer software, Protein Construct Design. The Construct Design tool of Gene Composer is a separate window positioned below the Alignment Viewer. To start a Construct Design session, the user defines a Base Construct from the Alignment Viewer (human protein sequence with black highlighted box), whose sequence is presented schematically (green bar) with a sliding window (green box) that delimits the amino acid sequence of the portion of the Base Construct within the sliding window (sequence above the green bar). The Alignment Viewer and Construct Design Tool are coordinated to move with each other as the user conducts various construct design operations across the Base Construct. Desired truncation end points are set by placing the cursor (red line in alignment) at desired sequence positions and inserting a right or left pointer for N-terminal and C-terminal truncations, respectively. The user may also create mutations within the amino acid sequence either as a single amino acid change (empty square), insertions (filled triangle above the inserted amino acids), deletions (filled, inverted triangle), or a mutation pool defining multiple mutations at a single site (dotted line above the desired changes). Once the desired construct modifications have been defined, the user can combine and permute any desired set of truncations and mutations to generate virtual constructs shown in the lower Construct Design window. Each construct is given a unique Construct ID and Construct Name according to a standardized schema that describes the N- and C-terminal residue numbers and other features.