Method and apparatus for codon determining

• US 7,702,464 B1
• Filed: 08/30/2002
• Issued: 04/20/2010
• Est. Priority Date: 08/21/2001
• Status: Expired due to Term

• Current Assignee: Codexis, Inc.
• Original Assignee: Maxygen Inc.
• Inventors: Cavet, Guy, Govindarajan, Sridhar, Gustafsson, Claes, Emig, Robin A., Minshull, Jeremy S., Fox, Richard John
• Primary Examiner(s): Clow; Lori A
• Application Number:
  US10/232,770
• Time in Patent Office: 2,790 Days
• Field of Search: 702/19, 702/20, 435/6
• US Class Current: 702/19
• 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 35/10 Design of libraries
• CPC Class Codes: G16C 20/60 In silico combinatorial chemistry

Abstract

Computer processing methods and/or systems for minimizing and/or optimizing data strings in accordance with rules and options. Minimized data strings can represent data sequences important in certain biologic analyses and/or syntheses. In specific embodiments, a request is generated by a user at a client system and received by a server system. The server system accesses initial data indicated or provided by the client system. The server system then performs an analysis to minimize the data needed for further reactions. In specific embodiments, a server can use proprietary methods or data at the server side while protecting those proprietary methods and data from access by the client system.

Claims

1. A method of providing degenerate oligonucleotide data using one or more logic processing systems, the method comprising:

receiving one or more indications of initial digital data from a user, said initial digital data indicating one or more polypeptide input sequences;

receiving options digital data from the user, said options data indicating one or more processing and/or input and/or output options for said sequences;

backtranslating said one or more polypeptide input sequences using one or more of said logic processing systems to create a set of backtranslated oligonucleotides;

using one or more items of said options digital data to affect said backtranslating, said options digital data affecting said backtranslating by specifying or varying input and/or output and/or processing of said backtranslating;

determining a set of degenerate oligonucleotides from said set of backtranslated oligonucleotides;

recombining and forward translating said set of degenerate oligonucleotides to produce systematically varied libraries of said one or more polypeptide input sequences; and

transmitting, using one or more of said systems, digital data representing said set of degenerate oligonucleotides to the user.

2. The method of claim 1 further comprising:

after receiving said indications of initial digital data indicating one or more polypeptide input sequences, generating one or more user interfaces including indications allowing the user to specify positional options data regarding positions in one or more of said input sequences;

presenting said one or more interfaces to the user; and

registering user actions indicating the positional options data regarding said one or more positions.

3. The method of claim 2 wherein:

said receiving and said transmitting are performed over a communications network;

said receiving and said transmitting are performed between a client system and a server system;

said backtranslating is performed under control of said server system;

said determining is performed under control of said server system;

said transmitting is performed under control of said server system;

said presenting is performed under control of said client system; and

said registering is performed under control of said client system.

4. The method of claim 1 wherein said receiving and said transmitting are performed over a communications network.

5. The method of claim 4 wherein said receiving and said transmitting are performed between a client system and a server system.

6. The method of claim 1 wherein said initial digital data comprises data representing two or more aligned polypeptide sequences.

7. The method of claim 1 wherein said initial digital data comprises data representing two or more unaligned polypeptide sequences and further comprising using an alignment algorithm to align said sequences.

8. The method of claim 1 further comprising:

during said backtranslating and/or said determining, accessing one or more analysis routines, wherein the details of operation of said analysis routines are not revealed to the user.

9. The method of claim 1 further comprising:

during said backtranslating and/or said determining, accessing one or more sets of intermediate data, wherein said intermediate data are not revealed to the user.

10. The method of claim 1 wherein said method is performed entirely on one or more information processing devices, with no in-vitro or in-vivo analysis or synthesis steps.

11. The method of claim 1 further comprising:

at said one or more logic processing systems ensuring that said initial digital data is kept secret and is not accessible to any operators of said computer system.

12. The method of claim 1 further comprising producing one or more nucleic acids by in vitro recombination, which nucleic acids are encoded using said transmitted data to synthesize.

13. The method of claim 1, wherein transmitting digital data representing said set of degenerate oligonucleotides to the user comprises displaying on a display said set of degenerate oligonucleotides.

14. The method of claim 1, wherein said recombining is performed digitally.

15. The method of claim 1, further comprising transmitting, using one or more of said systems, digital data representing said systematically varied libraries to the user.

16. A method of providing minimum degenerate oligonucleotides, the method comprising:

receiving one or more indications of initial digital data from a user at one or more of logic processing systems, said initial digital data indicating one or more polypeptide sequences;

receiving options digital data from the user at one or more of said systems, said options data indicating one or more processing options for said one or more polypeptide sequences;

backtranslating said one or more polypeptide sequences using one or more of said systems;

digitally determining using one or more of said systems a set of degenerate oligonucleotides;

recombining and forward translating to produce systematically varied libraries of said one or more polypeptide sequences or related polypeptides;

delivering a synthesized product to the user.

17. The method of claim 16 wherein said synthesized product comprises a library of synthesized oligonucleotides corresponding to said digitally determined set.

18. The method of claim 16 wherein said synthesized product comprises a library of synthesized oligonucleotides corresponding to said digitally determined set, with further characteristics of said library selected to facilitate physically recombining and combining said library.

19. The method of claim 16 further comprising:

performing a recombination reaction using said synthesized oligonucleotides;

translating the products of said recombination reaction to a plurality of polypeptide sequences that are systematically varied as a result of prior steps; and

wherein said synthesized product comprises a library of said systematically varied polypeptide sequences.

20. The method of claim 16 further comprising:

performing a recombination reaction using said synthesized oligonucleotides;

translating the products of said recombination reaction to a plurality of polypeptide

sequences that are systematically varied as a result of prior steps;

selecting from said plurality of systematically varied polypeptide sequences for a desired sequence characteristic;

wherein said synthesized product comprises one or more selected polypeptide sequences.