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

A method of identifying improved polypeptide or nucleic acid sequences, the method comprising:

• (a) receiving data identifying sequences of two or more parental polypeptides or parental nucleic acids that encode the polypeptides;
• (b) generating a multivariate sequence activity model from said sequences and associated activities of said parental polypeptides or parental nucleic acids;
• (c) using the multivariate sequence activity model to identify one or more oligonucleotides for recombination;
• (d) recombining the one or more oligonucleotides identified in (c) to produce recombined oligonucleotides;
• (e) screening at least some of the recombined oligonucleotides produced in (d) to select one or more of the recombined oligonucleotides;
• and
• (f) performing (a)-(e) recursively using selected recombined nucleic acids from (e) as identified sequences in (a) to identify an improved polypeptide or nucleic acid sequences.

A computer program product comprising a non-transitory machine readable medium having instructions for identifying improved polypeptide or nucleic acid sequences, the instructions comprising:

• (a) code for receiving data identifying sequences of two or more parental polypeptides or parental nucleic acids that encode the polypeptides;
• (b) code for generating a multivariate sequence activity model from said sequences and associated activities of said parental polypeptides or parental nucleic acids;
• (c) code for using the multivariate sequence activity model to identify one or more oligonucleotides for recombination;
• (d) code for receiving data identifying one or more of the recombined oligonucleotides produced from the one or more oligonucleotides identified in (c) and selected by screening;
• and
• (e) performing (a)-(d) recursively using identified recombined nucleic acids from (d) as identified sequences in (a) to identify an improved polypeptide or nucleic acid sequences.