Unlock instant, AI-driven research and patent intelligence for your innovation.

System and method for aligning a genome sequence considering mismatches

A base sequence and alignment system technology, applied in sequence analysis, biochemical equipment and methods, genomics, etc., can solve the problem of short fragment diversification length and achieve the effect of maintaining accuracy

Inactive Publication Date: 2014-12-24
SAMSUNG SDS CO LTD
View PDF7 Cites 0 Cited by
  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

However, for the base sequence alignment algorithm in the prior art, the tolerance value of the error is only mechanically applied according to the value (fixed value) set by the sequencer manufacturer or the user, but fails to consider the short fragments produced. Since the tolerance value of the error is variably adopted due to the characteristic, there is a problem that the length of the output short fragment tends to be diversified and its length is also increasing, which cannot be reflected.

Method used

the structure of the environmentally friendly knitted fabric provided by the present invention; figure 2 Flow chart of the yarn wrapping machine for environmentally friendly knitted fabrics and storage devices; image 3 Is the parameter map of the yarn covering machine
View more

Image

Smart Image Click on the blue labels to locate them in the text.
Viewing Examples
Smart Image
  • System and method for aligning a genome sequence considering mismatches
  • System and method for aligning a genome sequence considering mismatches
  • System and method for aligning a genome sequence considering mismatches

Examples

Experimental program
Comparison scheme
Effect test

Embodiment Construction

[0027] Hereinafter, specific embodiments of the present invention will be described with reference to the drawings. However, this is just an example, and the present invention is not limited thereto.

[0028] When describing the present invention, if it is considered that the specific description of the known technology related to the present invention may cause unnecessary confusion to the gist of the present invention, the detailed description will be omitted. In addition, terms described later are terms defined in consideration of functions in the present invention, and may vary depending on users, operator's intentions, practices, and the like. Therefore, it should be defined based on the contents of the entire specification.

[0029] The technical idea of ​​the present invention is determined by the claims, and the following embodiments are only a means for effectively explaining the technical idea of ​​the present invention to those with ordinary knowledge in the techni...

the structure of the environmentally friendly knitted fabric provided by the present invention; figure 2 Flow chart of the yarn wrapping machine for environmentally friendly knitted fabrics and storage devices; image 3 Is the parameter map of the yarn covering machine
Login to View More

PUM

No PUM Login to View More

Abstract

A system and method for aligning a genome sequence considering mismatches are provided. The system, according to one embodiment of the invention, for aligning the genome sequence includes an error bound calculation unit configured to calculate an error bound of a read according to a length of the input read, a comparison unit configured to calculate an error number estimate of the read and compare the error bound with the calculated error number estimate, and an alignment unit configured to perform a global alignment of the input read with a reference sequence when the comparison result shows that the calculated error number estimate is less than or equal to the error bound.

Description

technical field [0001] Embodiments of the present invention relate to a base sequence alignment technique used in genetic information interpretation work. Background technique [0002] The base sequence alignment algorithm refers to an algorithm for mapping (mapping) short fragments (reads) generated by a sequencing machine (or sequencer) used to generate base sequences to a known reference sequence (Reference Sequence). [0003] Base sequence alignment between a reference sequence and a short fragment sequence is basically based on exact matching using the homology (homology) of the base sequences. However, due to errors in the sequencing process and polymorphism in the genetic information of living organisms, an alignment method that allows a certain degree of error (mismatch) is actually necessary in the base sequence alignment algorithm. Existing base sequence alignment algorithms are configured to allow errors within respectively prescribed ranges. [0004] In additio...

Claims

the structure of the environmentally friendly knitted fabric provided by the present invention; figure 2 Flow chart of the yarn wrapping machine for environmentally friendly knitted fabrics and storage devices; image 3 Is the parameter map of the yarn covering machine
Login to View More

Application Information

Patent Timeline
no application Login to View More
Patent Type & Authority Applications(China)
IPC IPC(8): G06F19/18G16B30/10
CPCG16B30/00G16B30/10G16B99/00G16B20/00C12Q1/6869
Inventor 朴旻壻
Owner SAMSUNG SDS CO LTD