Fuzzy-based Spectral Alignment for Correcting DNA Sequence from Next Generation Sequencer

Kana Saputra S, Wisnu Ananta Kusuma, Agus Buono

Abstract


Next generation sequencing technology is able to generate short read in large numbers and in a relatively short in single running programs. Graph based DNA sequence assembly used to handle these big data in assembly step. The graph based DNA sequence assembly is very sensitive to DNA sequencing error. This problem could be solved by performing an error correction step before the assembly process. This research proposed fuzzy inference system (FIS) model based spectral alignment method which can detect and correct DNA sequencing error. The spectral alignment technique was implemented as a pre-processing step before the DNA sequence assembly process. The evaluation was conducted using Velvet assembler. The number of nodes yielded by the Velvet assembler become a measure of the success of error correction. The results shows that FIS model based spectral alignment created small number of nodes and therefore it successfully corrected the DNA reads.

Keywords


DNA Sequencing Error, Fuzzy Inference System Model, Next Generation Sequencing, Spectral Alignment, Velvet.

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References


Rogers K. New Thinking about Genetics. New York: Britannica Educational Publishing. 2011: 132.

Chong ML, Ku CS, Wu M, Soong R. Characterising Somatic Mutations in Cancer Genome by Means of Next-generation Sequencing. 2012. In: eLS. John Wiley & Sons, Ltd: Chichester.

Chevreux B. MIRA: An Automated Genome and EST Assembler. German Cancer Research Center Heidelberg, Department of Molecular Biophysics. 2005: 18.

Kelley DR, Michael CS, Steven LS. Quake: Quality-Aware Detection and Correction of Sequencing Errors. Genome Biology. 2010.

Miller JR, Koren S, Sutton G. Assembly Algorithms for Next-Generation Sequencing Data. Genomics. 2010; 95(6): 315–327.

Yang X, Chockalingam SP, Aluru S. A Survey of Error-Correction Methods for Next-Generation Sequencing. Journal of Briefing in Bioinformatics. 2012.

Pevzner PA, Tang H, Waterman MS. An Eulerian Path Approach to DNA Fragment Assembly. Proceedings of the National Academy of Sciences. 2001; 98(17): 9748–9753.