Methods of populating data structures for use in evolutionary simulations

• US 8,589,085 B2
• Filed: 03/29/2012
• Issued: 11/19/2013
• Est. Priority Date: 10/12/1999
• Status: Expired due to Fees

• Current Assignee: Codexis, Inc.
• Original Assignee: Codexis Mayflower Holdings, LLC (Codexis, Inc.)
• Inventors: Selifonov, Sergey A., Stemmer, Willem P. C.
• Primary Examiner(s): Dejong, Eric S
• Application Number:
  US13/434,261
• Publication Number:
  US 20120252684A1
• Time in Patent Office: 600 Days
• Field of Search: None
• US Class Current: 702/27
• 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 method of identifying molecules represented by concatenated strings, said method comprising:

i) providing a collection of two or more different initial character strings representing two or more initial biological molecules into a computer system associated with a synthesis machine;

ii) using the computer system, selecting at least two substrings from said collection of the two or more different initial character strings;

iii) using the computer system, concatenating the at least two selected substrings to form product strings;

iv) using the computer system, selecting one or more product biological molecules for synthesis, wherein the one or more product biological molecules are represented by one or more of the product strings; and

v) synthesizing the one or more product biological molecules using the synthetic machinery.

2. The method of claim 1, further comprising:

vi) adding additional initial character strings to the collection of the two or more different initial character strings, wherein the additional initial character strings encode segments of a subset of the one or more product biological molecules selected in v); and

vii) repeating operations ii)-v) using the collection of initial character strings, which now contains the added additional initial character strings.

3. The method of claim 1, further comprising assaying the one or more product biological molecules to determine one or more properties of the one or more product biological molecules.

4. The method of claim 3, further comprising selecting a subset of the one or more product biological molecules based on results of assaying the one or more product biological molecules.

5. The method of claim 4, wherein selecting is based on a characteristic selected from the group consisting of:

a temperature stability, a level of enzymatic activity, a pH level in a solution, one or more solubility limits, and one or more affinity limits.

6. The method of claim 1, further comprising expressing one or more proteins encoded by the one or more product biological molecules.

7. The method of claim 6, further comprising screening the one or more expressed proteins for one or more properties.

8. The method of claim 7, further comprising selecting a subset of the one or more product biological molecules based on results of screening the one or more expressed proteins.

9. The method of claim 1, wherein the one or more of the product strings are selected in iv) based on a parameter selected from the group consisting of one or more molecular weight limits, one or more free energy limits in a buffer system, one or more contact surface limits with a target molecule or a surface, one or more net charge limits in a buffer system, one or more predicted PK limits, one or more predicted PI limits, a secondary form, and a tertiary form.

10. The method of claim 1, wherein the one or more of the product strings representing the one or more product biological molecules have greater than 50% sequence identity with at least one of the initial character strings.

11. The method of claim 1, wherein the one or more of the product strings representing the one or more product biological molecules have greater than 75% sequence identity with at least one of the initial character strings.

12. The method of claim 1, wherein the one or more of the product strings representing the one or more product biological molecules have greater than 85% sequence identity with at least one of the initial character strings.

13. The method of claim 1, wherein the one or more of the product strings representing the one or more product biological molecules have greater than 90% sequence identity with at least one of the initial character strings.

14. The method of claim 1, wherein the one or more of the product strings representing the one or more product biological molecules have greater than 95% sequence identity with at least one of the initial character strings.

15. The method of claim 1, wherein the two or more initial biological molecules comprise a nucleic acid.

16. The method of claim 15, wherein the nucleic acid has a nucleic acid sequence encoding a naturally occurring protein.

17. The method of claim 1, further comprising encoding the two or more initial biological molecules into the initial character strings.

18. The method of claim 17, wherein the two or more encoded biological molecules comprises two or more amino acid sequences.

19. The method of claim 18, wherein the two or more amino acid sequences comprise an amino acid sequence encoding a naturally occurring protein.

20. The method of claim 1, wherein the initial character strings have at least 30% sequence identity with each other.

21. The method of claim 1, wherein selecting the at least two substrings comprises selecting at least one substring from the initial character string such that ends of the at least one substring occur in string regions of about 3 to about 20 characters in the initial character string that have higher sequence identity with the corresponding region of another of said initial character strings than an overall sequence identity between the two initial character strings.

22. The method of claim 1, wherein selecting the at least two substrings comprises selecting substrings such that ends of said substrings occur in predefined motifs of about 4 to about 8 characters.

23. The method of claim 1, wherein selecting the at least two substrings comprises:

aligning two or more of said initial character strings to maximize pairwise identity between the two or more substrings of the initial character strings; and

selecting a character that is a member of an aligned pair of the two or more substrings for an end of one of the two or more substrings.

24. The method of claim 1, further comprising randomly altering one or more character in the initial character strings prior to selecting the at least two substrings.

25. The method of claim 1, further comprising randomly altering one or more character in the one or more product strings prior to selecting the one or more product biological molecule.

26. The method of claim 1, further comprising randomly selecting and altering one or more occurrences of a particular preselected character in the initial character strings prior to selecting the at least two substrings.

27. The method of claim 1, further comprising randomly selecting and altering one or more occurrences of a particular preselected character in the one or more product strings prior to selecting the one or more product biological molecule.

28. The method of claim 1, wherein selecting the at least two substrings from said initial character strings comprises random substring selection.

29. The method of claim 1, wherein selecting the at least two substrings from said initial character strings comprises uniform substring selection.

30. The method of claim 1, wherein selecting at least two substrings from said initial character strings comprises motif-based selection.

31. The method of claim 1, wherein selecting at least two substrings from said initial character strings comprises alignment-based selection.

32. The method of claim 1, wherein selecting at least two substrings from said initial character strings comprises frequency-biased selection.

33. The method of claim 1, wherein synthesizing the one or more product biological molecules comprises chemical synthesis.

34. The method of claim 1, wherein synthesizing the one or more product biological molecules comprises recombinant synthesis.

35. The method of claim 1, wherein synthesizing the one or more product biological molecules comprises a PCR-based assembly.

36. The method of claim 1, further comprising shuffling the one or more product biological molecules to produce one or more shuffled biological molecules.

37. The method of claim 36, further comprising screening the one or more shuffled biological molecules to produce one or more new molecules.

38. The method of claim 1, wherein the synthetic machinery comprise a high-throughput system.

39. A method of identifying molecules represented by concatenated strings, said method comprising:

i) encoding two or more biological molecules to provide a collection of two or more different initial character strings, wherein the two or more biological molecules comprise homologous natural sequences;

ii) selecting at least two substrings from said collection of the two or more different initial character strings;

iii) concatenating the at least two selected substrings to form one or more product strings; and

iv) selecting a subset of product strings from the one or more product strings based a desired property; and

v) identifying preserved structural motifs based on comparison of character strings in the subset of product strings and the initial character strings.

40. A method of designing crossover oligonucleotides for forming chimeric junctions, the method comprising:

i) selecting substrings from parent strings representing nucleic acid sequences of two or more parent nucleic acids;

ii) receiving length and overlap information for the oligonucleotides;

iii) creating a matrix of oligonucleotides having defined crossovers based at least in part of the selection of the substrings and the length and overlap information; and

iv) synthesizing a library of oligonucleotides from the matrix.