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Method for establishing phylogenetic tree aiming at target gene of target organism

A technology of phylogenetic tree and target gene, applied in the field of establishment of phylogenetic tree

Inactive Publication Date: 2011-02-02
王颖
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Problems solved by technology

[0006] At present, the research on phylogenetic trees mainly focuses on the development of software and its connection with databases. The existing phylogenetic tree establishment methods are mostly based on the enhancement of software functions and the combination setting of multi-threshold optimization. Improving the Establishment Method of Phylogenetic Tree from the Perspective of Database Optimal Utilization

Method used

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  • Method for establishing phylogenetic tree aiming at target gene of target organism
  • Method for establishing phylogenetic tree aiming at target gene of target organism
  • Method for establishing phylogenetic tree aiming at target gene of target organism

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Embodiment

[0025] This study exemplifies the method of the present invention using the broccoli cellulose synthase (CesA) gene as the target gene.

[0026] 1. Data acquisition

[0027] Download the ls model of the cellulose synthase domain (PF03552) from the Pfam website, search and download it to the local Arabidopsis thaliana (Arabidopsis thaliana) through the hmmsearch function (default parameter) of HMMER2.3.2 : http: / / www.arabidopsis.org / ), rice (Oryza sativa: http: / / rice.plantbiology.msu.edu / ), Populus trichocarpa ： http: / / genome.jgi-psf.org / Poptr1_1 / Poptr1_1.home.html ), grapes (Vitis vinifera: http: / / www.genoscope.cns.fr / externe / Genome Browser / Vitis / ) protein database containing the protein sequence of this domain, all sequences with a threshold E≤0.001 are considered as members of the supergene family.

[0028] At the NCBI website and the EST library of flowering plants (The Floral Genome Project, http: / / fgp.bio.psu.edu / ) using AtCesA1, AtCesA3, AtCesA6, AtCesA8 ge...

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Abstract

The invention relates to a method for establishing a phylogenetic tree aiming at a target gene of a target organism. The method comprises the following steps of: 1) acquiring data; 2) comparing and analyzing sequences; and 3) establishing the phylogenetic tree, wherein the step 1) is finished by downloading a structure domain of a protein of the target gene, acquiring a sequence which contains the structure domain by searching a biological protein database of which genomes and proteomes are sequenced, and searching a protein sequence of a kindred plant by using the target gene of an organism of which the genomes and the proteomes are sequenced. Because the method of the invention comprises the steps and in particular combines the phylogenetic relationships of species with the database of which the genomes and the proteomes are sequenced, a more accurate phylogenetic tree can be established.

Description

technical field [0001] The invention relates to a method for analyzing genetic information, in particular to a method for establishing a phylogenetic tree. Background technique [0002] In the study of biological evolution and systematic classification, a tree-like branched graph is often used to represent the relationship between various organisms. This tree-like branched graph is called a phylogenetic tree (phylogenetic tree) , also called a phylogenetic tree), referred to as a phylogenetic tree. A dendrogram constructed by comparing the numerical values ​​of biological macromolecular sequence differences is called a molecular dendrogram. The ends of the branches of the phylogenetic tree and the connecting points of the branches are called knots, which represent biological groups, and the knots at the ends of the branches represent the species that are still alive. Phylogenetic trees can have time scales, or use branch length changes between knots to represent sequence d...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): C12Q1/68G06F17/30
Inventor 王颖
Owner 王颖
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