Biological species identification method based on genetic barcode

An identification method, bar code technology, used in special data processing applications, instruments, electrical digital data processing, etc.

Inactive Publication Date: 2012-01-25
JILIN UNIV
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

Although the development of science and technology has solved many important biological problems in maintaining biodiversity to ensure the safety of biological population...

Method used

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  • Biological species identification method based on genetic barcode
  • Biological species identification method based on genetic barcode
  • Biological species identification method based on genetic barcode

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0109] Example 1: Identification of Campylobacter jejuni subspecies NCTC11168 bacillus

[0110] We identify the subspecies NCTC11168 of the Campylobacter jejuni family. According to the method proposed in the present invention, the gene barcode image of the Campylobacter jejuni subspecies NCTC11168 bacillus is produced, preprocessed, vertically segmented, horizontally retrieved, and cut the gene fragment of the foreign insertion species , and finally calculate the acquaintance with the species in the prokaryotic database, and obtain the similarity measure of Campylobacter jejuni subsp. Table 3 shows:

[0111] Table 2: Similarity measures between NCTC11168 bacillus and the same family of bacteria

[0112] Campylobacter jejuni subsp. NCTC11168

[0113] Table 3: Similarity measure between NCTC11168 bacillus and heterophyletic bacteria

[0114] Hidden Acidophilus JF-5

[0115] It can be seen from Table 2 that the similarity measure between Campylobacter jejun...

Embodiment 2

[0116] Example 2: Identification of Chlamydia trachomatis D / UW-3 / CX

[0117] We selected Chlamydia trachomatis D / UW-3 / CX to do the second group of species identification and recognition experiments, and made and processed the gene barcode image of Chlamydia trachomatis D / UW-3 / CX according to the method proposed in the present invention , and finally calculate the acquaintance with the species in the prokaryotic database, and get the similarity measure between Chlamydia trachomatis D / UW-3 / CX and the same family of bacteria as shown in Table 4. Chlamydia trachomatis D / UW-3 / CX and The similarity measures of other alien bacteria are shown in Table 5:

[0118] Table 4: Similarity measure of Chlamydia trachomatis D / UW-3 / CX and the same family of bacteria

[0119] Chlamydia trachomatis D / UW-3 / CX

[0120] Table 5: Similarity measure between Chlamydia trachomatis D / UW-3 / CX and heterophyletic bacteria

[0121] Hidden Acidophilus JF-5

[0122] It can be seen from Ta...

Embodiment 3

[0123] Example 3: Haemophilus influenzae Rd KW20

[0124] We selected Haemophilus influenzae Rd KW20 to do the third group of species identification and recognition experiments. According to the method proposed by the present invention, the gene barcode image of Haemophilus influenzae Rd KW20 was produced, processed, and finally calculated with the species in the prokaryotic database Similarity, the similarity measure of Haemophilus influenzae Rd KW20 and the same family of bacteria is shown in Table 4, and the similarity measure of other heterogeneous bacteria is shown in Table 5:

[0125] Table 6: Similarity measure between Haemophilus influenzae Rd KW20 and the same family of bacteria

[0126] Haemophilus influenzae Rd KW20

[0127] Table 7: Similarity measures between Haemophilus influenzae Rd KW20 and heterogeneous bacteria

[0128] Thermotoga maritima MSB

[0129] It can be seen from Table 6 that the similarity measure between Haemophilus influenzae ...

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Abstract

The invention discloses a biological species identification method based on a gene barcode, which comprises the following steps of: 1. the production of a gene barcode image and a gene barcode image database: DNA (deoxyribonucleic acid) nucleotide sequences of 617 prokaryotes are downloaded from a website http://www. ncbi. nlm. nih. gov /, and the gene barcode image of species to be identified is produced according to the prior art; 2. the pre-processing of the gene barcode image: the gray scale of [0, L] of the gene barcode image is stretched to [0,255] by gray scale stretching, and the contrast of the gene barcode image is enhanced by gray scale enhancement; 3. the retrieval of foreign gene fragments of the gene barcode image: the longitudinal division of the gene barcode image is carried out, and the horizontal foreign gene fragments are searched; 4. species identification: the similarity quantity between the two species is determined, namely, the spatial distance between the two species is determined, and the species identification and result output are carried out according to the similarity quantity.

Description

technical field [0001] The invention relates to a method for identifying biological species, more specifically, the invention relates to an automatic species classification and identification method based on gene barcodes. Background technique [0002] Species identification and classification belong to the category of traditional biological taxonomy, and the identification and classification of species is the basis and premise of scientific research. Although the development of science and technology has solved many important biological problems in maintaining biodiversity to ensure the safety of biological populations, protecting species and preventing the epidemic of infectious diseases, it is still a scientific problem to be solved if we want to successfully identify and describe species . In April 2002, the German Association for Science put forward the idea of ​​establishing a DNA-based taxonomic system covering all biological groups. He also proposed the concept of ...

Claims

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Application Information

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IPC IPC(8): G06F19/10
Inventor 刘富侯涛康冰李丁园李扬
Owner JILIN UNIV
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