Double-sided genome segment filling method and device based on segment contiguous group

A filling method and genome technology, applied in the field of genetic engineering, can solve the problems of inability to apply double-sided genome fragment filling and completion, etc.

Pending Publication Date: 2021-04-09
SHANDONG JIANZHU UNIV
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  • Abstract
  • Description
  • Claims
  • Application Information

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Problems solved by technology

But these two algorithms can only solve the two-sided genome fragment population based on common sequences, and cannot...

Method used

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  • Double-sided genome segment filling method and device based on segment contiguous group
  • Double-sided genome segment filling method and device based on segment contiguous group
  • Double-sided genome segment filling method and device based on segment contiguous group

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Embodiment Construction

[0067] First, the concepts of arrangement, sequence, fragment contig, slot, largest missing gene string, common gene, contiguous missing string, contradictory common gene, etc. are explained.

[0068] Permutation: Given a gene set Σ, if the elements in Σ appear only once in P, then P is called permutation, and c(P) represents the set of elements in permutation P.

[0069] Sequence: Given a gene set Σ, if the elements in Σ appear multiple times in A, then A is called a sequence, and c(A) represents the set of elements in sequence A.

[0070] Adjacency: Given two sequences A=a 1 a 2 a 3 …a n , B=b 1 b 2 b 3 …b n , if a i a i+1 =b j b j+1 (or a i a i+1 =b j+1 b j ), where a i a i+1 ∈P A , b j+1 b j ∈P B . we call a i a i+1 and b j b j+1 match each other. at P A and P B Among the largest matching pairs, the pair a with matching relationship i a i+1 is called a common adjacency in A with respect to B

[0071] Breakpoint: pair a that does not have a m...

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Abstract

The invention discloses a genome segment filling method and device based on a segment contiguous group. The method comprises the following steps: calculating to obtain a deletion gene; classifying the maximum deletion gene string; merging the maximum deletion gene strings meeting the conditions; searching a Type-1 type string, and executing a Type-1 string insertion algorithm; searching for a Type-3-II type string without slot, and executing a no-slot-Type-3-II string insertion algorithm; searching Type-2 and Type-3 type strings, processing a common adjacency relation related to the contradictory common gene, and executing Type 2& 3-string insertion algorithm. Herein, the calculation is carried out based on the fragment contigs, the form is more general, and application is wider; the filling method is high in search speed and high in filling efficiency, can reduce the time and space complexity of genome segment filling based on the segment contiguous group, and improves the sensitivity and specificity of filling.

Description

technical field [0001] The invention relates to a method and a device for filling double-sided genome fragments based on fragment contigs, and belongs to the technical field of genetic engineering. Background technique [0002] With the continuous development of gene sequencing technology, the scale and speed of sequencing have been greatly improved, and the cost of sequencing has also been effectively reduced. However, it is still difficult to obtain a complete genome sequence only by gene sequencing. Under normal circumstances, the whole genome sequence is obtained by obtaining a large number of base sequences through a gene sequencer, and then assembling these short gene fragments into larger gene fragments (fragment contigs) through computer-related technology, namely the splicing algorithm, and determining The arrangement order of all fragment contigs in the genome, and the interval distance between each fragment contig, so as to obtain a larger gene structure - the gen...

Claims

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Application Information

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IPC IPC(8): G16B25/10
CPCG16B25/10
Inventor 柳楠李春良李胜华朱永琦李晓峰郑晶玲尤宝山王向辉
Owner SHANDONG JIANZHU UNIV
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