Method and system for polynucleotide synthesis
First Claim
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.
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Abstract
Methods and systems for automated polynucleotide synthesis design are provided. Example embodiments provide an Automated Polynucleotide Synthesis Design System (“APSDS”), which automatically generates a synthesis design for a designated target sequence specification. In one embodiment, the APSDS comprises a synthesis design engine, user interface support, a synthesis rules data repository, and a synthesis data repository. The APSDS automatically generates a synthesis design by receiving a target sequence(s) specification, generating a potential synthesis design, evaluating the potential design against synthesis rules, and when the evaluation indicates that the potential design is not successful according to the synthesis rules, adjusting the design to generate a new potential synthesis design and repeating the process of evaluating and adjusting until a potential synthesis design is found that satisfies the synthesis rules or until no solution is found.
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Citations
41 Claims
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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:
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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. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23)
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24. A computer-readable memory medium containing instructions for controlling a computer processor, when executed, to automatically generate a design for synthesizing a designated target double-stranded polynucleotide molecule according to a convergent synthesis technique, by performing a method comprising:
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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, generating the indication of the 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. - View Dependent Claims (25, 26, 27, 28, 29, 30, 31, 32)
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33. A computer system for generating a design for synthesizing a designated target double-stranded polynucleotide molecule according to a convergent synthesis technique, comprising:
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a synthesis rule data repository that contains a plurality of synthesis criteria for synthesizing fragments according to the convergent synthesis technique; a synthesis design engine that is configured to, decompose 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; retrieve at least one of the plurality of synthesis criteria from the synthesis rule data repository; automatically determine whether the potential double-stranded fragments satisfy the at least one synthesis criteria and generate an indication of the determination; when the indication indicates that the potential fragments do not satisfy the synthesis criteria, automatically adjust the fragment definitions of the plurality of potential fragments thereby adjusting at least one joint of the designated target molecule and repeat the automatic determination of whether the potential fragments satisfy the synthesis criteria, the generation of the indication of the determination, and the automatic adjustment of the fragment definitions until the generated indication indicates that the plurality of potential fragments will synthesize properly to create the designated polynucleotide molecule; and generate 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; and a synthesis design data repository that receives and stores the generated design output. - View Dependent Claims (34, 35, 36, 37, 38, 39, 40, 41)
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Specification