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Gene sequence optimization method suitable for high expression of pichia pastoris

A technology of gene sequence and optimization method, which is applied in the field of gene sequence optimization with high expression of Pichia pastoris, can solve problems such as difficult to obtain optimal gene sequence and large amount of information

Active Publication Date: 2021-01-26
FUJIAN NORMAL UNIV
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Problems solved by technology

Gene sequence optimization based on codon pair bias requires a large amount of information, and conventional manual methods are difficult to obtain the optimal gene sequence

Method used

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  • Gene sequence optimization method suitable for high expression of pichia pastoris
  • Gene sequence optimization method suitable for high expression of pichia pastoris

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Embodiment Construction

[0014] The present invention will be further described in detail below in conjunction with the accompanying drawings and specific embodiments.

[0015] A gene sequence optimization method suitable for high expression of Pichia pastoris, comprising the following steps:

[0016] Step 1: Read in the protein sequence to be expressed, wherein the protein sequence is represented by 20 amino acid abbreviations, each letter represents an amino acid, and its abbreviation is opposite to the 26 letters from A to Z, where B, J, O, U, X, Z letters do not correspond to amino acids. and a list of the codons corresponding to the amino acids.

[0017] Step 2: According to the codon combination weights, establish the codon combination preference matrix Tran, the codons in the left row of the matrix represent the amino acids that may appear at the current position in the sequence, and the codons in the right column represent the amino acids that may appear at the next position in the current po...

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Abstract

The invention discloses a gene sequence optimization method suitable for high expression of pichia pastoris. The gene sequence optimization method comprises the following steps of 1) reading a proteinsequence to be expressed, and processing; 2) establishing a codon transformation matrix according to the sequential combination weight of the codons; 3) defining a graph G, dividing the graph G inton layers according to the number n of amino acids contained in a protein sequence to be expressed, and connecting one edge of each layer of node to the next layer of node; 4) designing a maximum weight array Max Weigh [i, j]; 5) traversing from the last but one layer of the graph G to the first layer of the graph G, initializing the MaxWeigh [i, j] of the i layer of the current layer as a negativevalue, and updating the MaxWeigh element of the current layer; and 6) traversing from the first layer to the last layer of the graph G, and outputting a codon combination with the maximum weight through the calculated MaxWeigh [i, j], namely an optimized sequence. The gene sequence is optimized through the preference of the pichia pastoris codon pair, so a problem that the candidate path of the optimized sequence is exponentially increased is fully solved.

Description

technical field [0001] The invention relates to the technical field of biological information processing, in particular to a gene sequence optimization method suitable for high expression of Pichia pastoris. Background technique [0002] Pichia pastoris, a unicellular eukaryote ( Pichia pastoris ) expression system has become one of the most important exogenous protein expression systems due to its characteristics of both eukaryotes and prokaryotes. Because different hosts have a preference for the use of synonymous codons (codons encoding the same amino acid), the rare codons in the coding sequence of foreign proteins affect the translation rate and thus hinder their expression in host cells. Pichia pastoris is no exception, and Pichia pastoris also has a strong preference for synonymous codon usage. In order to improve the expression of foreign proteins in Pichia pastoris, the coding sequence needs to be optimized. The traditional method is to replace the synonymous codo...

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G16B30/00
CPCG16B30/00
Inventor 黄义德林劼林尧江育娥
Owner FUJIAN NORMAL UNIV
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