Design and development of DNA fragment assembly using IWP method

Author

Hassan, Haitham ; Majid, Zulkifli Abd ; Halim, Abdul Karimi ; Ibrahim, Amin

Author_Institution

Fac. of Electr. Eng., Univ. Teknol. MARA, Shah Alam, Malaysia

fYear

2013

fDate

19-20 Aug. 2013

Firstpage

63

Lastpage

68

Abstract

From time to time, researchers always try to improve algorithm for DNA fragment assembly that using de Bruijn graph. A de Bruijn graph is one of graph theoretical approach that based on short words (k-mers) that is ideal for high coverage, very short read (25-50bp) data sets. Therefore, the content of this paper proposed the development of DNA fragment assembly by using one of method that applied de Bruijn graph to construct complete a sequence, called Idury Waterman and Pevzner method. The algorithm was developed using Verilog HDL in Xilinx ISE Design Suite 14.2. The simulation used VCS Synopsys tool. The simulation result shows that it is tally with the theoretical analysis and was presented well in this paper.

Keywords

DNA; biology computing; graph theory; hardware description languages; DNA fragment assembly; IWP method; Idury Waterman and Pevzner method; VCS synopsys tool; Verilog HDL; Xilinx ISE design suite 14.2; de Bruijn graph; graph theoretical approach; k-mers; short read data sets; Assembly; Control systems; DNA; Genomics; Hardware design languages; Sequential analysis; Simulation; DNA fragment assembly; Idury Waterman Pevzner method; de Bruijn graph; eulerian path;

fLanguage

English

Publisher

ieee

Conference_Titel

Control and System Graduate Research Colloquium (ICSGRC), 2013 IEEE 4th

Conference_Location

Shah Alam

Print_ISBN

978-1-4799-0550-8

Type

conf

DOI

10.1109/ICSGRC.2013.6653277

Filename

6653277