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Primer design developing method of length polymorphism sign based on restriction enzyme digestion database-establishing pair-end sequencing

A paired-end sequencing and length polymorphism technology, applied in the field of bioinformatics, can solve the bottleneck of Indel labeling technology and the absence of reference sequences, etc., and achieve the effect of reducing sequencing costs and simplifying complexity

Active Publication Date: 2012-12-19
SHANGHAI MAJORBIO BIO PHARM TECH
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Problems solved by technology

But for those non-model organisms, basically there is no reference sequence
In the absence of a reference sequence, the traditional method of finding Indel markers has a technical bottleneck

Method used

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  • Primer design developing method of length polymorphism sign based on restriction enzyme digestion database-establishing pair-end sequencing
  • Primer design developing method of length polymorphism sign based on restriction enzyme digestion database-establishing pair-end sequencing
  • Primer design developing method of length polymorphism sign based on restriction enzyme digestion database-establishing pair-end sequencing

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Experimental program
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Effect test

Embodiment

[0063] Embodiment specific operation process:

[0064] The sequencing data obtained by the RAD-PE sequencing of the two parents were filtered according to the sequencing quality value, N content, and whether it contained restriction end sequences, and unqualified sequencing sequences were removed. The effective data statistics obtained are shown in Table 1.

[0065]

[0066] Table 1. Effective data statistics of gourd RAD-PE sequencing

[0067] According to the sequencing sequence of the enzyme-cleaved end of the sequenced individual genome, the information of the two parental piles is respectively generated by using the identity of the sequence. Filter out the results with a sequencing depth of 1 for the restriction end sequence. Figure 10 The distribution map of RAD sequence sequencing depth is shown, and the statistics of the results are shown in Table 2.

[0068] gourd sample Number of RAD sequences Average sequencing depth of RAD sequences male pare...

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Abstract

The invention discloses a primer design developing method of a length polymorphism sign based on restriction enzyme digestion database-establishing pair-end sequencing. Sequencing data of RAD (restriction site associated DNA) pair-end sequencing is processed by adopting a bioinformatics analysis method, therefore, Indel locus information on an RAD sequencing segment is searched, the bottleneck of being lack of a reference sequence in a model organism is broken through, the complexity of a genome is simplified, and the sequencing cost is reduced.

Description

technical field [0001] The invention relates to a primer design method for genome length polymorphism markers. Specifically, it is a primer design and development method for length polymorphism markers based on pair-end sequencing of restriction enzyme digestion library construction; in the absence of reference sequences, it can find the Indel markers between individuals and design primers at both ends . It belongs to the technical field of bioinformatics. This has important implications for the study of non-model organisms that lack reference sequences. Background technique [0002] InDel (insertion-deletion) insertion-deletion marker refers to the difference in the genome between the two parents. Compared with the other parent, there is a certain number of nucleotide insertions or deletions in the genome of one parent. The acquisition of Indel locus information can have many important applications, such as constructing genetic maps, genotyping, molecular marker-assisted...

Claims

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Application Information

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IPC IPC(8): G06F19/18
Inventor 郑泽群任一陶晔胡秋萍黄华生
Owner SHANGHAI MAJORBIO BIO PHARM TECH
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