Methods for making character strings, polynucleotides and polypeptides having desired characteristics
First Claim
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1. A computer program product comprising a machine readable medium on which is provided program code for identifying a set of oligonucleotides for use in a physical recombination procedure, the program code comprising:
- (a) code for providing one or more parental character strings representing one or more polynucleotides or polypeptides;
(b) code for manipulating the one or more parental character strings by applying a genetic operator to generate one or more derivative character strings; and
(c) code for selecting a set of character substrings from the one or more derivative character strings, which character substrings have sequences that identify the set of oligonucleotides for in vitro recombination.
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Abstract
“In silico” nucleic acid recombination methods, related integrated systems utilizing genetic operators and libraries made by in silico shuffling methods are provided.
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Citations
21 Claims
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1. A computer program product comprising a machine readable medium on which is provided program code for identifying a set of oligonucleotides for use in a physical recombination procedure, the program code comprising:
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(a) code for providing one or more parental character strings representing one or more polynucleotides or polypeptides;
(b) code for manipulating the one or more parental character strings by applying a genetic operator to generate one or more derivative character strings; and
(c) code for selecting a set of character substrings from the one or more derivative character strings, which character substrings have sequences that identify the set of oligonucleotides for in vitro recombination. - View Dependent Claims (2, 3, 4, 5)
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6. A computer program product comprising a machine readable medium on which is provide program code for identifying a set of oligonucleotides for use in a physical recombination procedure, the program code comprising:
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(a) code for providing two or more parental character strings representing one or more polynucleotides or polypeptides, which character strings, when aligned for maximum identity, comprise at least one region of heterology;
(b) code for aligning the parental character strings;
(c) code for manipulating the one or more parental character strings by applying a crossover operator to computationally generate one or more derivative character strings; and
(d) code for computationally selecting, from the one or more derivative character strings, a set of character substrings having sequences that identify the set of oligonucleotides for in vitro recombination, wherein the selected set of character substrings identifies at least one oligonucleotide comprising a chimeric nucleic acid sequence that comprises subsequences from at least two of the parental character strings, wherein the subsequences from the at least two parental character strings are separated by a crossover point, and wherein the crossover point is selected from a region of identified pairwise homology. - View Dependent Claims (7, 8, 9, 10)
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11. A computer program product comprising a machine readable medium on which is provided program instructions for identifying a set of oligonucleotides for use in a physical recombination procedure, the program code comprising:
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(a) code for providing two or more parental character strings representing one or more polynucleotides or polypeptides, which character strings, when aligned for maximum identity, comprise at least one region of heterology;
(c) code for manipulating the one or more parental character strings by applying a crossover operator to computationally generate one or more derivative character strings; and
(d) code for computationally selecting, from the one or more derivative character strings, a set of character substrings having sequences that identify the set of oligonucleotides for in vitro recombination, wherein the selected set of character substrings identifies at least one oligonucleotide comprising a chimeric nucleic acid sequence that comprises subsequences from at least two of the parental character strings, and wherein the subsequences from the at least two parental character strings are separated by a crossover point.
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12. A method of generating a set of polynucleotide variants, the method comprising:
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(a) providing one or more parental character strings representing one or more polynucleotides or polypeptides;
(b) manipulating the one or more parental character strings by applying a genetic operator to computationally generate one or more derivative character strings;
(c) from the one or more derivative character strings, computationally selecting a set of character substrings;
(d) providing a set of oligonucleotides corresponding in sequence to the set of character substrings; and
(e) recombining the set of oligonucleotides in vitro to generate a set of polynucleotide variants. - View Dependent Claims (13, 14, 15, 16, 17, 18, 19, 20, 21)
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Specification