SYSTEMS AND METHODS FOR ENGINEERING NUCLEIC ACID CONSTRUCTS USING SCORING TECHNIQUES

Systems and methods are provided for defining a nucleic acid construct for integration at locus L of an organism. Nucleic acid requests are received each such request specifying a genetic change to L and expanded into component polynucleotides. In some embodiments the component polynucleotides are arranged into {AR ... AR} different arrangements each AR in {AR ... AR} defining a different arrangement of the component polynucleotides. In some embodiments a score S for each AR in {AR ... AR} is determined based on whether source constructs encoding a portion of ARi are physically present. In some embodiments an AR in {AR ... AR} is selected based on the score for AR. In some embodiments primer pairs are calculated to amplify the portions of AR not represented in the source constructs. In some embodiments the portions of AR amplified by the primer pairs and the portions of AR in the source constructs ordered by AR define the nucleic acid construct.