US 7,702,464 B1Granted

Method and apparatus for codon determining

AssigneeMaxygen, Inc.

InventorsRobin A. Emig, Richard John Fox, Claes Gustafsson, Sridhar Govindarajan, Jeremy S. Minshull, Guy Cavet

Life of this patent

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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.

Claims20

Dependent claims

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.

5 more elements

Dependencies are inferred from the claim text.

Facts

Application: 10/232,770Filed 30 Aug 2002 · continuation in part
Priority: 21 Aug 2001
Granted: 20 Apr 2010
Term ends: Not estimatedThe source records don’t support an estimate.

Classification8 codes

G16B 35/10
ICT specially adapted for in silico combinatorial libraries of nucleic acids, proteins or peptides: design of libraries
G16B 30/00
Ict specially adapted for sequence analysis involving nucleotides or amino acids
G16B 30/10
ICT specially adapted for sequence analysis involving nucleotides or amino acids: sequence alignment; Homology search
G16B 30/20
ICT specially adapted for sequence analysis involving nucleotides or amino acids: sequence assembly

Family

Application60/314,131Us provisional application · filed 21 Aug 2001
Application60/316,852Us provisional application · filed 31 Aug 2001
Application60/339,886Us provisional application · filed 1 Nov 2001
Application60/363,505Us provisional application · filed 9 Mar 2002
Application60/392,511Us provisional application · filed 27 Jun 2002
Application10/225,564Parent of this continuation-in-part · filed 20 Aug 2002
US 7,873,477 B1Related patent
US 7,702,464 B1This patent

From the US filing history. Foreign family members aren’t listed.