Design and development of DNA fragment assembly using IWP method

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...

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Bibliographic Details
Main Authors: Hassan, Hasniliati, Majid, Zulkifli Abd, Halim, Abdul Karimi, Ibrahim, Azlina
Format: Conference Proceeding
Language:English
Subjects:
Assembly
Control systems
de Bruijn graph
DNA
DNA fragment assembly
eulerian path
Genomics
Hardware design languages
Idury Waterman Pevzner method
Sequential analysis
Simulation
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Summary: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.
DOI:10.1109/ICSGRC.2013.6653277