Systems and methods for engineering nucleic acid constructs using scoring techniques

• Main Authors: HAWTHORNE BRIAN L, CHANDRAN SUNIL S, DEAN ERIK JEDEDIAH, PLATT DARREN M, DOLAN CHRISTOPHER, BISSELL MICHAEL W
• Format: Patent
• Language: English
• Published: 11.12.2012
• Subjects: CALCULATING; COMPUTING; COUNTING; ELECTRIC DIGITAL DATA PROCESSING; INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTEDFOR SPECIFIC APPLICATION FIELDS; INFORMATION STORAGE; INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIRCHEMICAL OR PHYSICAL PROPERTIES; MEASURING; PHYSICS; STATIC STORES; TESTING

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. The request are expanded into component polynucleotides which are then arranged into {AR1, . . . , ARm} different arrangements, each ARi in {AR1, . . . , ARm} defining a different arrangement of the component polynucleotides. A score Si for each ARi in {AR1, . . . , ARm} is determined based on whether source constructs encoding a portion ofARi are physically present. An ARf in {AR1, . . . , ARm} is selected based on the score for ARf. Primer pairs are calculated to amplify the portions of ARf not represented in the source constructs. The portions of ARf amplified by the primer pairs and the portions of ARf in the source constructs, ordered by ARf, define the nucleic acid construct.