Method and system using systematically varied data libraries

• US 7,873,477 B1
• Filed: 08/20/2002
• Issued: 01/18/2011
• Est. Priority Date: 08/21/2001
• Status: Expired due to Term

• Current Assignee: Codexis, Inc.
• Original Assignee: Codexis Mayflower Holdings, LLC (Codexis, Inc.)
• Inventors: Govindarajan, Sridhar, Ness, Jon E., Gustafsson, Claes, Emig, Robin A., Minshull, Jeremy S.
• Primary Examiner(s): Clow; Lori A
• Application Number:
  US10/225,564
• Time in Patent Office: 3,073 Days
• Field of Search: None
• US Class Current: 702/19
• 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 20/50 Mutagenesis
• CPC Class Codes: G16B 35/00 ICT specially adapted for in silico combinatorial libraries of nucleic acids, proteins or peptides
• CPC Class Codes: G16B 35/10 Design of libraries
• CPC Class Codes: G16B 50/00 ICT programming tools or database systems specially adapted for bioinformatics
• CPC Class Codes: G16C 20/60 In silico combinatorial chemistry

Abstract

Methods and systems for providing biological results in the form of systematically varied libraries of sequences or as data representing sequences or physical preparations of systematically varied libraries and/or selections from systematically varied libraries.

Claims

1. A method of providing biological data using a communication network comprising:

sending from a server system to a client system over said communication network a set of instructions for displaying, on a user interface of the client system, one or more diversity generation operations available for execution at the server system;

receiving initial data from the client system over said communication network at a server system, said initial data indicating initial biologic sequence characteristics of one or more initial biologic molecules and a request for performing at least one of the one or more diversity generation operations;

sending a confirmation to the client system that the request is complete, said confirmation comprising a warning about proprietary information to be used in analyzing said initial data, said proprietary information is not accessible by the client system;

at said server system, analyzing said initial data and identifying a set of oligonucleotides corresponding to the initial biologic sequence characteristics that can be reassembled into new recombinant nucleic acids, wherein the proprietary information comprises the identified set of oligonucleotides;

at a destination associated with said server system, generating a physical preparation of a systematically varied library by recombining the identified set of oligonucleotides to generate new recombinant nucleic acids; and

delivering said physical preparation or sequence data corresponding to sequences in the systematically varied library to a destination associated with said client system.

2. The method of claim 1, wherein said initial data comprises oligonucleotide sequence data of one or more initial oligonucleotides.

3. The method of claim 1, wherein said initial data comprises polypeptide sequence data of one or more initial polypeptides.

4. The method of claim 1, wherein said initial data comprises molecular functional data indicating a desired function of a systematically varied library result.

5. The method of claim 1, wherein said initial data comprises structural data of one or more initial biologic molecules.

6. The method of claim 1, wherein said sequence data corresponding to sequences in the systematically varied library comprises digital data indicating positions or residues of an initial sequence that are good candidates for variation.

7. The method of claim 1, further comprising placing said physical preparation into a carrier for shipment to said destination associated with said client system.

8. The method of claim 7, wherein said carrier comprises a multiwell cassette.

9. The method of claim 7, wherein said carrier comprises a multiwell cassette, each well of said multiwall cassette identified by coordinate data, said coordinate data representing subsets of said systematically varied library.

10. The method of claim 1, wherein said identified set of oligonucleotides comprises a set of degenerate oligonucleotides.

11. The method of claim 1, wherein said identified set of oligonucleotides comprises a set of cross-over oligonucleotides.

12. The method of claim 1 further comprising:

at said server system, authenticating the identity of said client system.

13. The method of claim 1, further comprising:

at said server system, determining a fee for performing the at least one of the one or more diversity generation operations included in said initial data; and

at said server system, verifying client agreement to said fee.

14. The method of claim 1, further comprising, at said server system, ensuring that said initial data is kept secret and is not accessible to any operators of said server system.

15. The method of claim 1, wherein the one or more diversity generation operations available at the server system are selected from the group consisting of calculating shufflability of the one or more initial biologic molecules provided in the initial data, identifying the set of oligonucleotides, indentifying cross-over points, and identifying diversity.

16. The method of claim 1, wherein the server system is configured to receive information from one or more publicly available biologic sequence data banks.

17. The method of claim 1, further comprising requesting information from the one or more publicly available biologic sequence data banks and receiving the requested information from the one or more publicly available biologic sequence data banks.

18. The method of claim 17, wherein the information received from the one or more publicly available biologic sequence data banks is combined with the initial data received from the client system.

19. The method of claim 1, wherein the proprietary information comprises routines and/or subroutines corresponding to the one or more diversity generation operations available for execution at the server system.

20. The method of claim 1, wherein information about the systematically varied library is kept confidential at the server system with access limited to the client system.