Methods of populating data structures for use in evolutionary simulations

• US 8,170,806 B2
• Filed: 09/11/2009
• Issued: 05/01/2012
• 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): Zhou, Shubo
• Application Number:
  US12/557,746
• Publication Number:
  US 20100241640A1
• Time in Patent Office: 963 Days
• Field of Search: None
• US Class Current: 702/19
• 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 comprising a non-transitory computer readable medium, on which is stored instructions for:

i) encoding 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 ten subunits;

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

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

iv) determining sequence identities of at least one of the product strings relative to at least one initial character string;

v) selecting one or more product biological molecules for synthesis, wherein the one or more product biological molecules are encoded by one or more of the product strings;

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.

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

i) encoding two or more biological molecules into a data structure of initial character strings to provide a collection of two or more different initial character strings, wherein each of the two or more biological molecules comprises at least 10 subunits;

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

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

iv) obtaining one or more product biological molecules, wherein the one or more product biological molecules are encoded by one or more of the product strings having greater a predefined value of sequence identity with at least one initial string.

3. The method of claim 2, wherein obtaining the one or more product biological molecules comprises synthesizing the one or more product biological molecules.

4. The method of claim 3, wherein synthesizing the one or more product biological molecules comprises a recombinant method.

5. The method of claim 2, wherein obtaining the one or more product biological molecules comprises isolating the one or more product biological molecules.

6. The method of claim 2, further comprising assaying the one or more product biological molecules to determine one or more properties of the one or more product biological molecules.

7. The method of claim 6, 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.

8. The method of claim 7, wherein selecting is based on one or more of the following:

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.

9. The method of claim 7, further comprising:

encoding the subset of the one or more product biological molecules to provide one or more additional character strings; and

repeating operations ii), iii), and iv) using the one or more additional character strings as the initial character strings.

10. The method of claim 2, further comprising expressing one or more proteins encoded by the one or more product biological molecules.

11. The method of claim 10, further comprising screening the one or more expressed proteins for one or more properties.

12. The method of claim 11, further comprising selecting a subset of the one or more product biological molecules based on results of screening the one or more expressed proteins.

13. The method of claim 2, further comprising, prior to obtaining the one or more product biological molecules:

adding the one or more product strings formed in iii) to the data structure of the initial character strings; and

repeating operations ii) and iii) using a combination of the one or more product strings and the initial character strings.

14. The method of claim 2, further comprising, prior to obtaining the one or more product biological molecules:

selecting a subset of the one or more product strings formed in iii);

adding the subset of the one or more product strings to the data structure of the initial character strings; and

repeating operations ii) and iii) using a combination of the subset of the one or more product strings and the initial character strings.

15. The method of claim 2, further comprising, prior to obtaining the one or more product biological molecules, repeating operations ii) and iii) using the one or more product strings as the initial character strings.

16. The method of claim 2, further comprising, prior to obtaining the one or more product biological molecules:

selecting a subset of the one or more product strings; and

repeating operations ii) and iii) using the subset of the one or more product strings as the collection of initial character strings.

17. The method of claim 2, further comprising, prior to obtaining the one or more product biological molecules, selecting one or more of the product strings formed in iii).

18. The method of claim 17, wherein the one or more of the product strings are selected based on one or more of the following parameters:

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.

19. The method of claim 2, wherein the product strings corresponding to the one or more product biological molecules have greater than 50% sequence identity with at least one of the initial character strings.

20. The method of claim 2, wherein the product strings corresponding to the one or more product biological molecules have greater than 75% sequence identity with at least one of the initial character strings.

21. The method of claim 2, wherein the product strings corresponding to the one or more product biological molecules have greater than 85% sequence identity with at least one of the initial character strings.

22. The method of claim 2, wherein the product strings corresponding to the one or more product biological molecules have greater than 90% sequence identity with at least one of the initial character strings.

23. The method of claim 2, wherein the product strings corresponding to the one or more product biological molecules have greater than 95% sequence identity with at least one of the initial character strings.

24. The method of claim 2, wherein the two or more biological molecules comprise two or more nucleic acids.

25. The method of claim 24, wherein at least one of the two or more nucleic acids has a nucleic acid sequence encoding a naturally occurring protein.

26. The method of claim 2, wherein encoding the two or more biological molecules comprises encoding two or more amino acid sequences into the initial character strings.

27. The method of claim 26, wherein the two or more amino acid sequences comprise an amino acid sequence encoding a naturally occurring protein.

28. The method of claim 2, wherein the initial character strings have at least 30% sequence identity with each other.

29. The method of claim 2, 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.

30. The method of claim 2, 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.

31. The method of claim 2, 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.

32. The method of claim 2, wherein said method further comprises randomly altering one or more characters of said initial or product character strings.

33. The method of claim 32, wherein said method further comprises randomly selecting and altering one or more occurrences of a particular preselected character in said initial or product character strings.

34. The method of claim 2, wherein said encoding, selecting, or concatenating is performed in silico.

35. The method of claim 2, wherein selecting at least two substrings from said initial character strings comprises random substring selection.

36. The method of claim 2, wherein selecting at least two substrings from said initial character strings comprises uniform substring selection.

37. The method of claim 2, wherein selecting at least two substrings from said initial character strings comprises motif-based selection.

38. The method of claim 2, wherein selecting at least two substrings from said initial character strings comprises alignment-based selection.

39. The method of claim 2, wherein selecting at least two substrings from said initial character strings comprises frequency-biased selection.