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System and method for aligning genome sequence

A base sequence and sequence technology, which is applied in the field of analyzing the base sequence of the genome, to achieve the effects of improving accuracy, increasing the speed of global comparison, and improving the accuracy of mapping

Inactive Publication Date: 2014-05-14
SAMSUNG SDS CO LTD
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

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Problems solved by technology

However, methods in the prior art have limitations in meeting these requirements

Method used

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  • System and method for aligning genome sequence
  • System and method for aligning genome sequence
  • System and method for aligning genome sequence

Examples

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example 1

[0099] Example 1: When L=75, e=3,

[0100] Since f=15~15, so f=15,

[0101] s=4,

[0102] H=75–3×15–2×4=22.

example 2

[0103] Example 2: When L=100, e=4,

[0104] Since f=15~16, so f=16,

[0105] S=4,

[0106] H=100–4×16–2×4=36–8=28.

example 3

[0107] Example 3: When L=75, e=4,

[0108] Although f=15~12, since f should be greater than or equal to 15, so f=15,

[0109] s=4,

[0110] Although H=75–4×15–2×4=15-8=7, since f+s=19, the result will be H=19.

[0111] Figure 6 It is a block diagram of a base sequence alignment system 600 according to an embodiment of the present invention. The base sequence comparison system 600 according to one embodiment of the present invention is a device for performing the aforementioned base sequence comparison method, including: a fragment sequence generation unit 602, a screening unit 604, a mapping number calculation unit 606, and a comparison unit 608. The fragment sequence amplification unit 610.

[0112] The fragment sequence generation unit 602 generates a plurality of fragment sequences from short fragments obtained by a genome sequencer. As mentioned above, the fragment sequence generation unit 602 moves from the first base of the short fragment at a set interval and read...

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Abstract

A system and a method for aligning a genome sequence are provided. According to an embodiment of the present invention, the system for aligning a genome sequence includes a fragment sequence production unit configured to produce a plurality of fragment sequences from a read, a filtering unit configured to constitute a candidate fragment sequence group including only the fragment sequences mapped to a reference sequence among the plurality of produced fragment sequences, a mapping number calculation unit configured to divide the reference sequence into a plurality of sections and calculate total mapping numbers of the candidate fragment sequences for the sections, and an alignment unit configured to select the sections in which the calculated total mapping numbers are greater than or equal to a reference number and perform global alignment on the read with respect to the selected sections.

Description

technical field [0001] An embodiment of the present invention relates to a technique for analyzing the base sequence of a genome. Background technique [0002] The second-generation sequencing (NGS: Next Generation Sequencing) method for producing high-capacity short sequences is rapidly replacing the traditional Sanger (Sanger) sequencing method because of its low cost and the ability to quickly generate data. Also, various NGS sequence recombination programs have been developed with a focus on accuracy. However, with the recent development of second-generation sequencing technology, the cost of producing fragment sequences has been reduced to less than half of the past, and the amount of available data has increased. Therefore, it is necessary to develop a method that can accurately process high-capacity short sequences in a short time Technology. [0003] The first step of sequence recombination is to map the short fragments to the correct position of the reference sequ...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G06F19/22G16B30/10
CPCG16B30/00G16B30/10C12Q1/6869
Inventor 朴旻胥
Owner SAMSUNG SDS CO LTD
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