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Method based on repetitive sequence recognition for splicing sequencing data of whole genome

A whole-genome sequencing and repeating sequence technology, applied in the field of genetic engineering, can solve problems such as splicing errors in large genome data of higher animals and plants

Inactive Publication Date: 2002-07-24
北京六合华大基因科技有限公司
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Problems solved by technology

[0003] The purpose of the present invention is to propose a splicing method for whole genome sequencing data based on repetitive sequence identification, after analyzing the rules of the repetitive sequences in the genomes of higher animals and plants when using the "shotgun method" for sequencing, to solve the problem caused by repetitive sequences The problem of data splicing errors caused by large genomes of higher animals and plants, thus providing a reliable means for efficient and rapid whole-genome sequencing analysis of higher animals and plants using the "shotgun method"

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  • Method based on repetitive sequence recognition for splicing sequencing data of whole genome
  • Method based on repetitive sequence recognition for splicing sequencing data of whole genome
  • Method based on repetitive sequence recognition for splicing sequencing data of whole genome

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[0026] Below in conjunction with accompanying drawing, introduce each step of the inventive method in detail:

[0027] In order to identify repetitive sequences, the present invention first sets a minimum fragment length, generally set to 15bp-20bp, and repetitive sequences shorter than this length will not be considered. To simplify the model, it is assumed that all sequencing reads are equal in length, L.

[0028] The meaning of the parameters in the following formulas: G: total genome length, L: average effective read length of sequencing N: number of successful sequencing reactions, F: minimum fragment length for identification.

[0029] Count the occurrences of small non-repeated fragments in shotgun sequencing:

[0030] Define a random variable Y ik Describe the event that the above-mentioned DNA fragment of the specified length appears K times in the whole genome sequencing by the shotgun method:

[0031] If the number of occurrences of fragments starting from a ce...

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Abstract

A method based on repetitive sequence recognition for splicing the sequencing data of full-genome includes calculating the probability distribution of non-repetitive and repetitive fragments in sequencing data, determining the standard for recognizing repetitive sequences, shielding the repetitive sequences with said standard, splicing by group according to size of target genoma, restoring the N in big fragment back to original bases, finding out relative big fragments and the reading between them, linking them together, and sorting them to obtain the working block diagram of target genome. Its advantages are high efficiency and high accuracy.

Description

technical field [0001] The invention relates to a splicing method of whole genome sequencing data based on repetitive sequence recognition, which belongs to the technical field of genetic engineering. Background technique [0002] Genomics is a comprehensive analysis of the complete set of genetic material of an organism to understand the function and role of genetic information from a holistic perspective. The most important step is to determine the complete set of genetic information of the organism, that is, to know the sequence of all nucleic acid bases of the organism, which is the so-called whole genome sequencing analysis. At present, the whole genome sequencing mainly adopts two strategies: 1. "Hierarchical cloning method", that is, the larger genome is first broken into medium-sized fragments (150kb~300kb) and cloned, and then the medium fragments are broken into small fragments (1kb~300kb). 3kb) for sequencing, and finally for data splicing by computer. For examp...

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Application Information

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IPC IPC(8): C12P19/34C12Q1/68
Inventor 李松岗王俊盖伊·王于军汪建杨焕明倪培相韩玉军黄显刚张建国胡咏武
Owner 北京六合华大基因科技有限公司
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