Species taxonomy method based on diversity comparisons of distances among amino acids in protein sequences

A protein sequence and amino acid technology, applied in sequence analysis, proteomics, genomics, etc., can solve the problems of not considering gaps, increased calculation amount, large error, etc., and achieve the effect of simple calculation method

CN105512512AActive Publication Date: 2016-04-20WEIFANG MEDICAL UNIV
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Patent Information

Authority / Receiving Office
CN · China
Patent Type
Applications(China)
Current Assignee / Owner
Publication Date
2016-04-20

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Abstract

The invention brings forward a species taxonomy method based on diversity comparisons of distances among amino acids in protein sequences. The method comprises following steps: S10, numbering each amino acid of a protein sequence; S20, calculating the distance between every two adjacent proteins of the same kind in each protein sequence; S30, counting frequency of different distances between every two adjacent proteins of the same kind in each protein sequence; and S40, comparing statistical data in a pair-wise sequence manner, setting up distance matrixes and performing species taxonomy by calculating phylogeny trees in generating systems based on distance matrixes. The species taxonomy method based on diversity comparisons of distances among amino acids in protein sequences has following beneficial effects: differences among amino acid in sequences are shifted to be those among distances of amino acid so that space is saved and no gap is required; and the method is easy and helps to simplify calculation amount.
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Description

technical field

[0001] The invention belongs to the field of species identification, in particular to a method for classifying species by comparing protein sequences with amino acid distance polymorphisms. Background technique

[0002] At present, according to the theory of evolution, if two protein sequences come from the same ancestor, there will be a certain degree of homology, and the closer the relative relationship, the higher the homology of the species, so it can be classified according to the sequence of amino acids in the protein sequence, and establish The phylogenetic tree of molecular evolution. At present, the Clustal algorithm proposed by Higgins and Sharp in 1988 is widely used. Firstly, multiple sequences are pairwise compared to construct a distance matrix to reflect the pairwise relationship between sequences, and then a phylogenetic tree is generated according to the distance matrix calculation. When two sequences are compared, the simplest case is to ig...

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Embodiment Construction

[0020] The following will clearly and completely describe the technical solutions in the embodiments of the present invention with reference to the accompanying drawings in the embodiments of the present invention. Obviously, the described embodiments are only some, not all, embodiments of the present invention. Based on the embodiments of the present invention, all other embodiments obtained by persons of ordinary skill in the art without creative efforts fall within the protection scope of the present invention.

[0021] Such as figure 1 As shown, the amino acid distance polymorphism comparison protein sequence of the present invention carries out the method for species classification, comprising the following steps:

[0022] S10: number each amino acid on the protein sequence;

[0023] S20: Calculate the distance between adjacent amino acids of the same type on the protein sequence;

[0024] S30: Count the number of occurrences of different distances between adjacent amin...