GENOME SEQUENCE MAPPING DEVICE AND GENOME SEQUENCE MAPPING METHOD THEREOF

• US 20130158885A1
• Filed: 11/08/2012
• Published: 06/20/2013
• Est. Priority Date: 12/14/2011
• Status: Abandoned Application

• Current Assignee: Electronics and Telecommunications Research Institute
• Original Assignee: Electronics and Telecommunications Research Institute
• Inventors: PARK, Chan Yong
• Application Number:
  US13/672,529
• Publication Number:
  US 20130158885A1
• Time in Patent Office: Days
• US Class Current: 702/20
• CPC Class Codes: G16B 30/00 ICT specially adapted for sequence analysis involving nucleotides or amino acids
• CPC Class Codes: G16B 30/10 Sequence alignment; Homology search
• CPC Class Codes: G16B 40/00 ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding

Abstract

Provided are a genome sequence mapping device and a genome sequence mapping method. The genome sequence mapping device may include a controller and a genome sequence analyzer configured to map target sequence data to reference sequence data. The genome sequence analyzer transforms the reference sequence data and the target sequence data into frequency domains to determine a position of the target sequence data to be mapped among the reference sequence data. The genome sequence mapping device calculates a correlation between reference sequence data and target sequence data in a frequency domain to immediately determine whether the reference sequence data and the target sequence data match each other.

Claims

1. A genome sequence mapping device comprising:

a controller; and

a genome sequence analyzer configured to map target sequence data to reference sequence data,

wherein the genome sequence analyzer transforms the reference sequence data and the target sequence data into frequency domains to determine a position of the target sequence data to be mapped among the reference sequence data.

2. The genome sequence mapping device as set forth in claim 1, wherein the genome sequence analyzer comprises a coder configured to code the reference sequence data and the target sequence data into binary data, respectively.

3. The genome sequence mapping device as set forth in claim 2, wherein the coder configures to compose the reference sequence data and the target sequence data with computer-processable units, respectively.

4. The genome sequence mapping device as set forth in claim 2, wherein the genome sequence analyzer further comprises a Fourier transformer configured to perform a Fourier transform operation on the coded reference sequence data and the coded target sequence data.

5. The genome sequence mapping device as set forth in claim 4, wherein the genome sequence analyzer further comprises a correlation calculator configured to perform a correlation calculation operation on the Fourier-transformed reference sequence data and the Fourier-transformed target sequence data.

6. The genome sequence mapping device as set forth in claim 5, wherein the genome sequence analyzer further comprises an inverse Fourier transformer configured to inversely Fourier-transform a result value of the correlation calculation performed by the correlation calculator.

7. The genome sequence mapping device as set forth in claim 6, wherein the genome sequence analyzer further comprises an optimal position determiner configured to determine a position of the target sequence data to be mapped among the reference sequence data, based on a result of the inverse Fourier transform.

8. The genome sequence mapping device as set forth in claim 7, wherein the optimal position determiner determines a position of the target sequence data to be mapped among the reference sequence data, based on values of a plurality of peak points of the result of the inverse Fourier transform.

9. The genome sequence mapping device as set forth in claim 1, wherein the target sequence data is genome sequence data produced by the next-generation sequencing scheme.

10. The genome sequence mapping device as set forth in claim 9, wherein length of the target sequence data is less than that of the reference sequence data.

11. A genome sequence mapping method comprising:

transforming reference sequence data and target sequence data into frequency domains, respectively;

performing a correlation calculation on the reference sequence data transformed into the frequency domain and the target sequence data transformed into the frequency domain; and

determining a matching position of the target sequence data among the reference sequence data, based on a result of the correlation calculation.

12. The genome sequence mapping method as set forth in claim 11, further comprising:

coding the reference sequence data and the target sequence data into binary data, respectively.

13. The genome sequence mapping method as set forth in claim 12, further comprising:

converting the binary-coded reference sequence data and the binary-coded target sequence data into computer-processable units, respectively.

14. The genome sequence mapping method as set forth in claim 11, wherein the computer-processable unit is a unit of byte.

15. The genome sequence mapping method as set forth in claim 11, further comprising:

performing inverse Fourier transform on a result of the correlation calculation after performing the correlation calculation.

16. The genome sequence mapping method as set forth in claim 15, wherein a step of the determining a matching position of the target sequence data among the reference sequence data includes determining a position of the target sequence data to be mapped among the reference sequence data, based on values of a plurality of peak points of the result of the inverse Fourier transform.

17. The genome sequence mapping method as set forth in claim 11, wherein the target sequence data is genome sequence data produced by the next-generation sequencing scheme.

18. The genome sequence mapping method as set forth in claim 11, wherein length of the target sequence data is less than that of the reference sequence data.