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Method for judging frame shift of gene sequence of cDNA library

A gene sequence and frameshift technology, applied in the field of gene analysis, can solve the problems of inability to guarantee the correct coding of proteins, error-prone, heavy workload, etc.

Pending Publication Date: 2021-11-02
SHANGHAI OE BIOTECH CO LTD
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  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

[0003] The construction of cDNA library generally utilizes the polyA tail of mRNA as the characteristic of polyA, and uses OligodT primers to reverse transcribe from the 3' end to the 5' end to obtain sscDNA; Since the position of the reverse transcription termination cannot be precisely controlled, there is no guarantee that the cDNA ligated into the vector will encode the correct protein
Therefore, in gene screening experiments using cDNA libraries (such as yeast two-hybrid cDNA library screening, subtractive library screening, etc.), after obtaining positive clones, it is impossible to directly detect whether the obtained positive clone cDNA is correctly encoded in the vector. Confirm the obtained cDNA sequence by first-generation sequencing and other methods, and then analyze the sequence results one by one whether the inserted sequence is frame-shifted, the process is cumbersome, the workload is heavy and error-prone

Method used

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  • Method for judging frame shift of gene sequence of cDNA library
  • Method for judging frame shift of gene sequence of cDNA library
  • Method for judging frame shift of gene sequence of cDNA library

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0066] Follow the steps below to align the cDNA sequences:

[0067] (1) Upload the sequence to be compared and the gene database to the host;

[0068] (2) Convert the sequence format to be compared to Fasta format;

[0069] (3) Align the sequence to be compared with the reference gene or protein sequence in the local database;

[0070] (4) Output the target gene that matches the gene to be compared according to the matching scoring value of the candidate gene and the gene to be compared. The comparison result is as figure 1 shown.

Embodiment 2

[0072] Follow the steps below to compare the cDNA sequences, the flow chart is as follows figure 2 Shown:

[0073] (1) Upload the sequence to be compared and the gene database to the host;

[0074] (2) Convert the sequence format to be compared to Fasta format;

[0075] (3) Set the display mode of the sequences to be compared to 1 row;

[0076] (4) Setting the library adapter sequence;

[0077] (5) Find and delete the upstream of the linker and the linker sequence in the sequence to be compared;

[0078] (6) Convert the cDNA sequence that removes the library linker to an amino acid sequence, compare it in the local protein database, and analyze the matching rate;

[0079] (7) output the gene with the highest comparison score as the optimal result, and the optimal result is the target gene;

[0080] (8) According to the set frameshift judgment rule, calculate whether the expression of the sequence to be compared in the vector is frameshifted;

[0081] (9) Output whether ...

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Abstract

The invention provides a method for judging frame shift of gene sequence of cDNA library, and belongs to the technical field of gene analysis. According to the method disclosed by the invention, the target sequences matched with the cDNA to be compared can be obtained in batches, the result of whether the cDNA is subjected to code shift in the carrier or not is detected according to the position number, the analysis efficiency is not influenced by the limitation of the maintenance of an open source database, the network speed and the like any more, and the gene comparison analysis efficiency is greatly improved.

Description

technical field [0001] The invention relates to the technical field of gene analysis, in particular to a method for judging the frameshift of a cDNA library gene sequence. Background technique [0002] A cDNA library is a kind of gene library, which refers to the cDNA fragment formed by reverse transcription of all the mRNA transcribed by a certain organism at a certain developmental stage, which is connected with a certain carrier and then transferred into the recipient cell to form a clone. gather. Unlike genomic DNA, which contains introns, cDNA may be difficult to express correctly. cDNA is easy to clone and amplify in large quantities. The desired target gene can be screened from the cDNA library and directly used for the expression of the target gene and transgenic research. The construction and screening of cDNA library has become an important method in the study of functional genomics, and it is one of the basic tools for discovering new genes and studying gene func...

Claims

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Application Information

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IPC IPC(8): G16B30/10G16B50/30
CPCG16B30/10G16B50/30
Inventor 张萍萍公光业肖云平李晖林博殷昊赵仕兰
Owner SHANGHAI OE BIOTECH CO LTD
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