Gene synthesis software
AssigneedeCODE biostructures, Inc.
InventorsLansing Stewart, Alex Burgin, John Walchli, Kathryn Hjerrild
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Abstract
Pieces of software and databases are used to facilitate the design and synthesis of genes. The synthesis techniques allow identification, quantification, transcription, translation, and manipulation of portions of the gene sequence represented as 0's and 1's in a computing system. These pieces of software and databases compile constraint information provided by a user to create synthetic genes to express proteins lacking disordered or variable regions and containing surface mutations that promote solubility and/or crystallization. Regions of the gene sequence that do not form stable structures can be removed and replaced by a short biological linker to improve crystallization of proteins.
Claims20
A computer system for synthesizing gene sequences, comprising:
- a gene specifier for specifying an amino acid sequence and a number of parameters including an expression system, a threshold to exclude rare codons, salt concentration, molar concentration, and target melting temperature;
- a back translator for translating the amino acid sequence into a nucleic acid sequence whose codons exclude rare codons and include codons with participating probabilities to allow them to appear in the nucleic acid sequence;
- and
- an oligonucleotide producer that processes the nucleic acid sequence to produce sets of oligonucleotides whose melting temperature is within proximity to the target melting temperature for synthesizing a gene sequence representing the nucleic acid sequence.
A computer-implemented method for synthesizing gene sequences, comprising:
- back translating an amino acid sequence to a nucleic acid sequence;
- and
- introducing stop codons into the nucleic acid sequence via silent mutations.
A computer-readable medium having instructions stored thereon to implement a method for synthesizing gene sequences, the method comprising:
- specifying an amino acid sequence and a number of parameters including an expression system, a threshold to exclude rare codons, salt concentration, molar concentration, and target melting temperature;
- translating the amino acid sequence into a nucleic acid sequence whose codons exclude rare codons and include codons with participating probabilities to allow them to appear in the nucleic acid sequence;
- and
- processing the nucleic acid sequence to produce sets of oligonucleotides whose melting temperature is within proximity to the target melting temperature for synthesizing a gene sequence representing the nucleic acid sequence.
Dependencies are inferred from the claim text.