Methods and compositions for polypeptide engineering

A method of producing a library comprising chimerized, defined polynucleotide sequences each of which comprises a defined number of polynucleotide segments that are assembled in an ordered fashion, the method comprising:

• a) generating a plurality of defined polynucleotide segments selected from aligned substrate nucleic acid sequences, wherein said substrate nucleic acids encode full-length enzymes, and wherein boundaries defining the polynucleotide segments are selected from the aligned substrate nucleic acid sequences;
• and
• b) reassembling said defined polynucleotide segments in order thereby producing the library of chimerized, defined polynucleotide sequences, such that said segments are reassembled in an ordered fashion to produce each chimerized, defined polynucleotide sequence encoding a full-length enzyme, each of which comprises a defined number of polynucleotide segments that are reassembled in an ordered fashion.