Patent ID: 7164992
Filing Date: 2007-01-16
Classification: G16B,G16C

Abstract:
1. A method in a computer system for automated generation of a design for synthesizing a designated target double-stranded polynucleotide molecule according to a convergent synthesis technique, comprising: decomposing the designated target molecule into a plurality of potential double-stranded fragments, each fragment having an associated fragment definition and having ends that will potentially ligate with ends of other fragments; automatically determining whether the potential double-stranded fragments satisfy a plurality of synthesis criteria for synthesizing fragments and generating an indication of the determination; when the indication indicates that the potential fragments do not satisfy the synthesis criteria, automatically adjusting the fragment definitions of the plurality of potential fragments thereby adjusting at least one joint of the designated target molecule and repeating the automatically determining whether the potential fragments satisfy the plurality of synthesis criteria, the generating the indication of determination, and the automatically adjusting the fragment definitions until the generated indication indicates that the plurality of potential fragments will synthesize properly to create the designated polynucleotide molecule; and generating a design output that indicates the polynucleotide sequences of the plurality of potential fragments as defined by the adjusted fragment definitions and an ordering for combining the plurality of polynucleotide sequences according to a convergent synthesis technique.