Methods for making character strings, polynucleotides and polypeptides having desired characteristics

• US 20080318795A1
• Filed: 10/31/2007
• Published: 12/25/2008
• Est. Priority Date: 01/19/1999
• Status: Active Grant

• Current Assignee: Codexis, Inc.
• Original Assignee: Maxygen Inc.
• Inventors: del Cardayre, Stephen, Tobin, Matthew, Patten, Phillip A., Giver, Lorraine J., Selifonov, Sergey A., Gustafsson, Claes, Minshull, Jeremy, Stemmer, Willem P.C.
• Granted Patent: US 7,904,249 B2
• Time in Patent Office: Days
• US Class Current: 506/1
• CPC Class Codes: B01J 2219/007 Simulation or vitual synthesis
• CPC Class Codes: G16B 10/00 ICT specially adapted for evolutionary bioinformatics, e.g. phylogenetic tree construction or analysis
• CPC Class Codes: G16B 15/00 ICT specially adapted for analysing two-dimensional or three-dimensional molecular structures, e.g. structural or functional relations or structure alignment
• CPC Class Codes: G16B 15/20 Protein or domain folding
• CPC Class Codes: G16B 20/00 ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• CPC Class Codes: G16B 20/20 Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
• CPC Class Codes: G16B 20/30 Detection of binding sites or motifs
• CPC Class Codes: G16B 20/50 Mutagenesis
• CPC Class Codes: G16B 30/00 ICT specially adapted for sequence analysis involving nucleotides or amino acids
• CPC Class Codes: G16B 30/10 Sequence alignment; Homology search
• CPC Class Codes: G16B 30/20 Sequence assembly
• CPC Class Codes: G16B 35/00 ICT specially adapted for in silico combinatorial libraries of nucleic acids, proteins or peptides
• CPC Class Codes: G16B 35/20 Screening of libraries
• CPC Class Codes: G16B 40/00 ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
• CPC Class Codes: G16B 40/10 Signal processing, e.g. from mass spectrometry [MS] or from PCR
• CPC Class Codes: G16C 20/60 In silico combinatorial chemistry

Abstract

In silico nucleic acid recombination methods, related integrated systems utilizing genetic operators and libraries made by in silico shuffling methods are provided.

Claims

1. A method of generating nucleic acids, the method comprising:

inputting a plurality of amino acid sequence character strings into a digital system; and

translating the amino acid character strings in the digital system into a plurality of nucleic acid character strings, wherein translated nucleic acid sequences are selected for one or more of;

species codon bias in a selected expression host, and optimized sequence similarity between the plurality of nucleic acid character strings.