Method for batch computing of evolutionary rate of orthologous genes of genome

A homologous gene and genome technology, applied in the field of batch calculation of the evolution rate of genome orthologous genes, can solve the difficulty of increasing the batch calculation of the evolution rate of genome orthologous genes, limit the use of non-biological information professionals, and restrict the field of molecular evolution Research and other issues to achieve the effect of making up for time-consuming and labor-intensive, fast, comprehensive and comprehensive parameters

Active Publication Date: 2016-03-23
JIANGSU ACADEMY OF AGRICULTURAL SCIENCES
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Problems solved by technology

However, when the program uses the maximum likelihood method to analyze the phylogenetic analysis of DNA or protein sequences, the background knowledge of the program involves quite complicated modern statistical theory and calculation methods, which is a great challenge for non-professional researchers; in addition, To ensure the operation of the yn00 program, it is necessary to perform a lot of pre-processing on the downloaded genome file, and finally convert it into an input file with a fixed format (such as figure 2 ), which not only increases the time-consuming use of the model, but also increases the difficulty of calculating the evolution rate of genome orthologous genes in batches, which greatly limits the use of this software by non-biological information majors and those with relatively weak computer foundations. Ultimately constrained their research in the field of molecular evolution

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  • Method for batch computing of evolutionary rate of orthologous genes of genome
  • Method for batch computing of evolutionary rate of orthologous genes of genome
  • Method for batch computing of evolutionary rate of orthologous genes of genome

Examples

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Embodiment 1

[0033] Example 1. Establishment of a method for calculating the evolution rate of genome orthologous genes in batches

[0034] The flowchart of the method for calculating the evolution rate of genome orthologous genes in batches provided by the present invention is shown in figure 1 , including the following steps:

[0035] (1) Using the InParanoid program for clustering based on the results of Blast pairwise comparisons, identify the orthologous genes in the Speci1 and Speci2 genomes (data sets A and B) to be tested, operate under the Linux system, and use default parameter settings Perform analysis; follow the steps below to obtain complete orthologous gene pair ID and score information files (C data set);

[0036] Steps to obtain the complete orthologous gene pair ID and score information file: Open the folder where the InParanoid software package "inparanoid.pl" file is located, and run the "perlinparanoid.plXXX1XXX2" command, where "XXX1" and "XXX2" represent A , the fil...

Embodiment 2

[0055] Example 2, using the method established in Example 1 to calculate the evolution rate of genes between Raymond cotton and Asian cotton genomes in batches

[0056] Enter the cotton genome project link (http: / / cgp.genomics.org.cn / ) database of the Cotton Research Institute of the Chinese Academy of Agricultural Sciences to download the genome sequence (13 chromosomes, 885Mb) and Asian cotton (Gossypium arboretum L.) (13 chromosomes, 1,746Mb), in the Windows system or local Linux computing server, the gene evolution rate between Raymond cotton and Asian cotton genomes was calculated. During the calculation process, the commonly used program names, operating environments and addresses involved are shown in Table 1. The specific operation steps of the calculation method are as follows:

[0057] 1) Carry out with reference to the step (1) of Example 1.

[0058] Using the InParanoid program to identify the orthologous genes between the genomes of Raymond cotton (data set A) a...

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Abstract

The invention discloses a method for batch computing of the evolutionary rate of orthologous genes of a genome. According to the method for batch computing of the evolutionary rate of the orthologous genes of the genome, an InParanoid program for clustering searching of orthologous genes after a paired comparing result is obtained based on Blast, an MUSCLE program based on multi-sequence comparative analysis and a PAML software package yn00 program for evaluating the synonymous and non-synonymous substitution ratio based on comparison between coding protein DNA sequences are comprehensively used, and the methods such as Perl scripting language programming are combined. It is proved through experiments that a method comparing system for batch computing of the evolutionary rate of the orthologous genes of the genome is good in repeat effect on various parameter values for detecting the genome and computing the evolutionary rate of the orthologous genes of the genome, high in speed and capable of easily achieving batch computing, automation and processing.

Description

technical field [0001] The invention belongs to the field of biotechnology, and relates to a method for calculating the evolution rate of genome orthologous genes in batches. Background technique [0002] In recent years, the vigorous development of sequencing technology has greatly promoted the research work in the field of genomics. The completion of the whole genome sequencing of many model organisms such as yeast, mouse, human, Arabidopsis and rice has made the analysis of the genetic components of the species genome more and more important, which in turn makes molecular evolution become a major field in computational biology and bioinformatics. It is an important part of emerging disciplines such as life sciences, and ranks among the most compelling fields in the life sciences. The calculation method of evolution rate is one of the basic tools in the research of this subject, which has greatly promoted the development of this subject. At present, the most commonly use...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G06F19/14G06F19/24G16B10/00
CPCG16B10/00G16B40/00
Inventor 郭月刘静杜建厂
Owner JIANGSU ACADEMY OF AGRICULTURAL SCIENCES
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