Methods for identifying sets of oligonucleotides for use in an in vitro recombination procedure

1. A method of identifying a set of oligonucleotides for use in an in vitro recombination procedure, the method comprising:

(a) receiving data identifying sequences of two or more parental polypeptides or parental nucleic acids that encode the polypeptides;

(b) selecting one or more cross-over sites on the sequences based on structural information about the parental polypeptides or polypeptides encoded by the parental nucleic acids; thereby defining one or more recombinant polypeptides or recombinant nucleic acids that result from cross-overs between the parental polypeptides or nucleic acids at the one or more cross-over sites;

(c) selecting at least one of the recombinant polypeptides or recombinant nucleic acids;

(d) identifying one or more oligonucleotides for in vitro recombination by choosing at least one portion of at least one of the recombinant polypeptides or recombinant nucleic acids selected in (c) which at least one portion identifies the one or more oligonucleotides for in vitro recombination; and

(e) outputting the identities of the one or more oligonucleotides for in vitro recombination,

wherein each of operations (a) through (e) is performed via a suitably programmed computer system.

2. The method of claim 1 , wherein the structural information employed in (b) comprises information depicting the three-dimensional structure of at least a portion of the parental polypeptides or polypeptides encoded by the parental nucleic acids.

3. The method of claim 1 , wherein (b) comprises selecting cross-over points that occur at points of overlapping amino acids in the parental polypeptides.

4. The method of claim 1 , wherein (b) comprises selecting cross-over points at sites that will preserve selected subunits, domains, or motifs in the parental polypeptides.

5. The method of claim 1 , wherein (b) comprises selecting cross-over points at sites chosen to maintain or disrupt one or more structural relationships between two or more amino acids in the parental polypeptides.

6. The method of claim 1 , further comprising performing an additional genetic operation on one or more of the parental or recombinant polypeptides or the parental or recombinant nucleic acids.

7. The method of claim 6 , wherein the genetic operation is selected from the group consisting of multiplication, mutation, fragmentation, and ligation.

8. The method of claim 1 , wherein the two or more parental polypeptides or parental nucleic acids comprise naturally occurring polypeptides or naturally occurring nucleic acids that encodes polypeptides.

9. The method of claim 1 , wherein the oligonucleotides identified in (d) are “bridging” oligonucleotides.

10. The method of claim 1 , further comprising aligning the two or more parental polypeptides or parental nucleic acids prior to computationally selecting one or more cross-over sites on the sequences.

11. The method of claim 1 , wherein the recombinant polypeptides or recombinant nucleic acids that result from the cross-overs comprise contiguous sequences of multiple amino acids or nucleotides from the two or more of the parental polypeptides or parental nucleic acids.