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Exploring method and exploring device for biological genome simple repeat sequence

A simple repetitive sequence and genome technology, applied in special data processing applications, instruments, electrical digital data processing, etc., can solve problems such as cumbersome and complex excavation processes

Inactive Publication Date: 2012-06-13
TOBACCO RES INST CHIN AGRI SCI ACAD
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

Although different software adopts different de-redundancy strategies, the mining process is relatively complex and cumbersome, requiring a large amount of statistical analysis and logical operations. So far, no redundant analysis algorithm has been seen.

Method used

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  • Exploring method and exploring device for biological genome simple repeat sequence
  • Exploring method and exploring device for biological genome simple repeat sequence
  • Exploring method and exploring device for biological genome simple repeat sequence

Examples

Experimental program
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Embodiment Construction

[0032] Such as figure 1 As shown, it is a schematic flow chart of the method for discovering the simple repeat sequence of the biological genome provided by the embodiment of the present invention, including the following steps:

[0033] Step 101, constructing a regular expression according to the characteristics of the simple repeat sequence SSR of the biological genome to be discovered;

[0034] Among them, the characteristics of the simple repeat sequence SSR of the biological genome that need to be discovered include:

[0035] The minimum length information of the motif in the simple repeat sequence SSR of the biological genome that needs to be discovered, the maximum length information of the motif, and the minimum number of repetitions information of the motif, wherein the motif refers to the motif in the SSR repeat unit.

[0036] The form of the regular expression constructed is: (.{i, j}?)(\1){k,}, wherein, i, j, k respectively represent the minimum length value of t...

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Abstract

The invention discloses an exploring method for a biological genome simple repeat sequence, which is characterized by comprising the following steps of: forming a regular expression according to the characteristics of the biological genome SSR (Simple Repeat Sequence) needed to be explored; analyzing a to-be-analyzed sequence according to the regular expression, judging whether the to-be-analyzed sequence contains a target SSR meeting the requirement of the regular expression, if so, outputting the target SSR; if not, displaying information about that the to-be-analyzed sequence contains no target SSR. Thus, the exploring method and the exploring device for the biological genome simple repeat sequence cannot generate redundant result in a SSR exploring process, so that the configuration complexity of the SSR exploring process is reduced, SSR exploring efficiency is improved and difficulty in development of SSR exploring software is reduced.

Description

technical field [0001] The invention relates to the technical field of SSR mining, in particular to a method and equipment for mining simple repeat sequences of biological genomes. Background technique [0002] SSR (Simple Sequence Repeats, simple repeat sequence) refers to the tandem repeat of 1 to 5 nucleotides in a DNA molecule. With its advantages of random distribution, high information content and polymorphism, co-dominance and Mendelian inheritance in animal and plant genomes, SSR is widely used in the construction of genetic maps, genetic diversity analysis, identification of kinship, DNA fingerprint construction and functional genes. Marking and other aspects have recognized advantages and application prospects. [0003] At present, the existing SSR mining algorithms are mostly based on character string mining, and then use statistical analysis methods to remove redundancy, which basically includes the following three steps: first, enumerate all possible base combi...

Claims

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Application Information

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IPC IPC(8): G06F19/24
Inventor 任民王志德刘艳华张兴伟牟建民
Owner TOBACCO RES INST CHIN AGRI SCI ACAD
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