Multi-gene family identification and evolution analysis method

A gene family and evolutionary analysis technology, applied in the field of biological information analysis, can solve the problems of limited analysis range, high cost, cumbersome operation, etc., and achieve the effect of mature analysis method, high accuracy and high efficiency

Active Publication Date: 2020-07-24
GUANGZHOU GENE DENOVO BIOTECH
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  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

These methods have a limited range of analysis and can only be used to discover new gene family members. They did not conduct comprehensive and in-depth analysis of known gene family members, nor did they use existing technologies and databases to mine more information, resulting in a certain degree of data waste.
Moreover, these methods need to use methods such as probe hybridization screening, PCR primer amplification, etc., and the genome library must be constructed in advance, which is costly, cumbersome to operate, low in input and output, and long in cycle

Method used

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  • Multi-gene family identification and evolution analysis method

Examples

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Embodiment 1

[0063] This example provides a cross-species, multi-dimensional, comprehensive multi-gene family identification and The method of evolutionary analysis, its technological process is as follows figure 1 shown, including the following steps:

[0064] Step 1, statistical gene sequence or protein sequence information;

[0065] Obtain the gene sequence or protein sequence information of the SMAD protein gene family of three species of turbot (Scophthalmus maximus), zebrafish (Danio rerio), and flounder (Paralichthys olivaceus).

[0066] Step 2, carry out identification and evolution analysis for the target species;

[0067] Step 2.1, protein gene family identification

[0068] (1) Compare the gene sequence of the SMAD gene family with the turbot genome, and analyze the structural annotation information of the gene, such as the location of the gene on the chromosome, the CDS sequence of the gene, exons, introns and other information.

[0069] (2) Translating the CDS sequence of ...

Embodiment 2

[0105] In this example, three fish species, turbot (Scophthalmus maximus), zebrafish (Danio rerio), and flounder (Paralichthys olivaceus), are taken as examples to provide a cross-species, multi-dimensional, comprehensive target species and close relatives. A method for identification and evolution analysis of multi-gene families of species, the technological process of which is as follows figure 1 shown, including the following steps:

[0106] Step 1, identifying protein gene families for related species;

[0107] The following is an analysis of the SMAD protein gene family of turbot (Scophthalmus maximus, sma) and its close relatives, zebrafish (Daniorerio, dre) and flounder (Paralichthys olivaceus, pol).

[0108] According to the reference genome information of the two species of zebrafish and flounder and their respective SMAD protein gene family information, the SMAD protein information and gene sequences of zebrafish and flounder species were analyzed respectively by us...

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Abstract

The invention provides a multi-gene family identification and evolution analysis method. The method is an independent analysis technology or a joint analysis technology for target species and homologous species. The independent analysis method comprises the steps of protein gene family identification, protein gene family structure information analysis, family gene member chromosome distribution analysis, replication gene event prediction, Motif analysis and protein gene family evolutionary tree analysis. The joint analysis method comprises the following analysis processes: protein gene familyidentification, protein gene family evolutionary tree analysis, Ka/Ks analysis, gene selective evolution analysis and colinearity analysis. The method does not need design of primers, PCR amplification and construction of a genome library; the analysis process is mature, the period is short, the yield is high; analysis results are confirmed through two databases of Pfam and SMART, and the accuracyrate is high; and the method is suitable for DNA sequencing data or protein sequences.

Description

technical field [0001] The invention relates to the field of biological information analysis of gene sequence information and protein sequences, in particular to a cross-species, multi-dimensional, comprehensive multi-gene family identification and systematic method for evolution analysis. Background technique [0002] A gene family is a group of genes derived from the same ancestor and produced two or more copies of a gene through gene duplication. They have obvious similarities in structure and function, encoding similar protein products. The exon sequences of genes in the same family are related, therefore, the proteins encoded by these genes have similar amino acid sequences, structural domains and functions, and these proteins are called protein families. At present, most commonly used gene family analysis methods only analyze one aspect of gene structure, replication type or evolutionary tree analysis, and there is no systematic and comprehensive bioinformatics analys...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G16B30/10G16B15/20
CPCG16B30/10G16B15/20
Inventor 高川陶勇夏昊强周煌凯艾鹏石悦
Owner GUANGZHOU GENE DENOVO BIOTECH
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