METHODS OF POPULATING DATA STRUCTURES FOR USE IN EVOLUTIONARY SIMULATIONS

• US 20100241640A1
• Filed: 09/11/2009
• Published: 09/23/2010
• Est. Priority Date: 10/12/1999
• Status: Active Grant

• Current Assignee: Codexis, Inc.
• Original Assignee: Maxygen Inc.
• Inventors: Selifonov, Sergey A., Stemmer, Willem P.C.
• Granted Patent: US 8,170,806 B2
• Time in Patent Office: Days
• US Class Current: 707/756
• CPC Class Codes: G06N 3/126 Evolutionary algorithms, e.g. genetic algorithms or genetic programming
• CPC Class Codes: G16B 10/00 ICT specially adapted for evolutionary bioinformatics, e.g. phylogenetic tree construction or analysis
• 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 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 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

Abstract

In particular, this invention provides novel methods of populating data structures for use in evolutionary modeling. In particular, this invention provides methods of populating a data structure with a plurality of character strings. The methods involve encoding two or more biological molecules into character strings to provide a collection of two or more different initial character strings; selecting at least two substrings from the pool of character strings; concatenating the substrings to form one or more product strings about the same length as one or more of the initial character strings; adding the product strings to a collection of strings; and optionally repeating this process using one or more of the product strings as an initial string in the collection of initial character strings.

Claims

1. A computer program product on a computer readable media comprising computer code that:

i) encodes two or more biological molecules into initial character strings to provide a collection of two or more different initial character strings wherein each of said biological molecules comprises at least about ten subunits;

ii) selects at least two substrings from said initial character strings;

iii) concatenates said substrings to form one or more product strings about the same length as one or more of the initial character strings;

iv) adds the product strings to a data structure to populate a data structure of product strings;

v) determines sequence identities of at least one of the product strings relative to at least one initial character string; and

vi) selects one or more product biological molecules for production, wherein the one or more product biological molecules correspond to one or more of the product strings.